Means for diagnosing, predicting or monitoring pneumocystis pneumonia

ABSTRACT

The application relates to means for diagnosing, predicting or monitoring Pneumocystis pneumonia (PCP). The means of the application are also suitable for determining or predicting the efficacy of a drug or treatment against PCP in a human patient. The means of involve the detection and/or quantification, more particularly the quantification, of the RNA transcripts of two different P. jirovecii mitochondrial genes. The first of said two P. jirovecii mitochondrial genes is the P. jirovecii gene, the sequence of which codes for the Cytb protein or the P. jirovecii mitochondrial Small Sub-Unit (mtSSU) gene. The second of said two P. jirovecii mitochondrial genes is a P. jirovecii gene, the sequence of which transcribes into a P. jirovecii ribosomal RNA, e.g., be the mitochondrial P. jirovecii Large Sub-Unit (mtLSU) gene.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.15/564,246, filed Oct. 4, 2017, which is the U.S. Natl. Stage ofInternational Appln. PCT/EP2016/058355, filed Apr. 15, 2016, whichclaims the benefit of European Appln. 15305562.9 filed Apr. 15, 2015,all of which are herein incorporated by reference in their entirety.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Dec. 15, 2021, isnamed B11232A_ST25.txt and is 24,543 bytes in size.

FIELD OF THE INVENTION

The application relates to means for diagnosing, predicting ormonitoring Pneumocystis pneumonia (PCP). The means of the applicationinvolve the detection and/or quantification, more particularly thequantification, of the RNA transcripts of two different P. jirovecilmitochondrial genes.

The means of the application are also suitable for determining orpredicting the efficacy of a drug or treatment against PCP in a humanpatient or for determining whether PCP regresses or has been treated ina human patient who has been diagnosed to have PCP and who is receivingor has received a drug or treatment against PCP.

BACKGROUND OF THE INVENTION

PneumoCystis Pneumonia (PCP) is an opportunistic infection due to theascomycetous fungus Pneumocystis jirovecii. This pathogen is specificfor humans whereas related species exists for other terrestrial mammals,and growing evidence suggest that P. jirovecii could be considered as acommensal of human respiratory tract. It lives and thrives at thesurface of the alveolar cells (type I pneumocytes) and can be foundtypically as two main forms: (i) the trophic form that undergo asexualmultiplication by binary fission and (ii) ascus (cyst) containing eightascospores that is the result of the sexual mode of replication. Thecomplete life cycle of Pneumocystis carinii has been studied in rats.Experiments in animals suggest that Pneumocystis is transmissible fromhost to host with immunocompetent individuals as the most importantreservoir and asci as the potential agent of transmission.Epidemiological and experimental data suggests that P. jirovecii is alsoa transmissible organism in humans. HIV-infected individuals with lowCD4 counts are at risk of developing PCP. Despite highly effectiveprophylaxis with cotrimoxazole (association of a Dihydrofolate reductaseinhibitor (trimethoprim) and of a sulfonamide antibiotic(sulfamethoxazole)) and highly active anti-retroviral treatments, PCPremains one of the most prevalent infections in patients with AIDS. PCPalso occurs in non-HIV immunocompromised patients, including patientswith hematological or solid malignancies, transplant recipients, andthose receiving immunosuppressive treatments for autoimmune orinflammatory diseases.

In non-HIV immunocompromised patients, PCP is typically more acute andsevere than in HIV patients. PCP diagnosis is also harder since theaverage fungal charge is lower in non-HIV patients than in HIV patients.

Overall, PCP carries a mortality rate of 35 to 55% in non-HIVimmunocompromised patients, compared to 10 to 20% in HIV-infectedpatients.

Diagnosis of PCP usually relies on microscopic demonstration of P.jirovecii in respiratory specimens using various staining methods thatincludes conventional staining (Calcofluor White. Toluidine Blue O,Gomori methamine, Giemsa staining) and anti-P. jiroveciiimmunofluorescence assays (IFA) (direct or indirect IFA). It is knownfor a long time that immunofluorescence is more sensitive thanconventional staining. Alternatively, in the 1990's, two methods havebeen developed: beta-D-glucan (BDG) detection and PCR.

The lack of sensitivity of microscopic methods due to low burden of P.jirovecii in non-HIV immunocompromised patients has justified thedevelopment of diagnostic PCR-based methods in the early 1990's todetect DNA in clinical samples rather than the microorganism itself.Initially. DNA detection aimed also at increasing sensitivity of P.jirovecii detection to avoid invasive procedure such as BronchoAlveolarLavage (BAL) in patients suspected of PCP with the ambition to useinduced sputa (IS) and/or upper respiratory specimens (URS,nasopharyngeal aspirate, oral washes or nasal swab) as diagnosticspecimens. These methods were more sensitive and reproducible thanmicroscopic detection (conventional staining and/or immunofluorescence),considered as gold-standard test in respiratory samples such asBronchoAlveolar Lavage Fluid (BALF) or induced sputa at that time.

Single (sPCR) and nested end point (nPCR) formats used initially for DNAdetection were progressively replaced by the quantitative real-time PCR(qPCR) format, where the PCR products is detected and quantified duringamplification without opening of the reaction tube. The main advantagesof this format are preventing false positives due to environmentalcontamination with previously amplified products, and to provide rapidquantitative results. Subgroup analysis regarding the PCR format wasperformed in the meta-analyses and showed higher sensitivity andspecificity in qPCR assays compared to the global analysis. In addition,recommendations for diagnostic PCR already exist, highlighting thenecessity to use real-time PCR format.

The difference in performance reported for different PCR assays could beexplained by the different DNA targets used for amplification and theprimer designs. Indeed, most of the authors have developed their ownprimers, although generally designed to amplify a multicopy gene, whichincrease the sensitivity compared to a single copy gene. The P.jirovecii mitochondrial Large Sub-Unit ribosomal RNA (rRNA) gene (mtLSU)is the most commonly used. The multicopy Major Surface Antigen (MSG)gene was also targeted in various reports. Multiple single copy nucleargene were also used such as 18S ribosomal DNA (rDNA), 5S rDNA, Internaltranscribed spacer (ITS), DHPS, KEX, HSP70, Beta-TUBulin (BTUB) andCDC2. Indeed, ribosomal RNA genes cluster is unique in Pneumocystis.

Comparison of analytical performance could be easily achieved using thequantification results of external quality controls. A comparison ofthree PCR assays using MSG (multicopy) and DHPS (single copy) targetgenes demonstrated the transferability of the results.

However, PCR revealed the possibility to detect Pneumocystis DNA inpulmonary specimens from immunocompromised individuals without clinicalsigns or symptoms of PCP. This phenomenon was called P. jiroveciicolonization or carriage. For this reason, PCR is not completelyaccepted as a diagnostic criterion for PCP, although the sensitivity ofPCR assays is higher than microscopy and PCR was cost-effective innon-invasive specimens.

One simple method to discriminate active Pneumocystis pneumonia from P.jirovecii carriage in respiratory samples of patients at risk of PCP isto determine quantitative thresholds. Since PCR is much more sensitivethan microscopy, to define thresholds for assessing the diagnosis iscrucial and cannot be performed without reliable quantification.

Real-time quantitative PCR refers to real-time PCR that is able toquantify the amount of DNA in the extract using calibration curves basedon reference DNA (plasmid), expressed as copy/volume unit. However,quantitative results can be expressed with other units. Alternatively,some authors use the crude qPCR results (as quantification cycle, Cq,Ct, or Cp), or some others translate it into a number of microorganismsbased on counts (for example trophic form equivalent). No internationalstandard qPCR assay and no threshold are currently consensual. Largeinternational studies, or at least prospective studies, are highlyneeded to allow technical validation of this tool. Thereafter, the useof qPCR for clinical interpretation of qPCR results would be possibleand validated.

For samples harboring positive IFA, qPCR and microscopic quantification,as evaluated as the number of cysts (often expressed as +, ++ or +++),gave similar results. When qPCR results are in congruence with IFA,there is little question about the interpretation of the results.However, there is an overlap around the sensitivity limit of IFA, withsome samples IFA negative and PCR positive whereas other samples are IFApositive with a lower P. jirovecii DNA content. A consensus of thelowest qPCR results corresponding to the IFA positive samples harboringthe lowest fungal load is almost impossible since IFA is dependent ofthe examiner and the quality of the sample. On the other end of thespectrum, there is little doubt about the interpretation of the qPCRnegative results. The negative predictive value of PCR assays hasreached a consensus. The only point to be checked is the correctamplification of the internal control to avoid false negative results.Discrepancies appear for the IFA-negative qPCR-positive results. Someauthors propose a grey zone. For instance, two cut-off values of 120 and1900 trophic form equivalent/mL were proposed to discriminate activepneumonia from carriage, with a grey zone between them.

There is a need for new means for diagnosing, predicting or monitoringPCP, more particularly for means, which discriminate PCP from P.jirovecil carriage. Therefore, we developed a new PCR method for thedetection of Pneumocystis RNA.

Our test is based on the detection and the quantification of the RNAtranscripts of two genes of Pneumocystis jirovecii in the BAL fluid ofpatients.

SUMMARY OF THE INVENTION

The application provides means, which are notably useful for diagnosing,predicting or monitoring Pneumocystis pneumonia (PCP).

The means of the application notably enable to discriminate a PCPpatient from a P. jirovecii carrier, who does not have or does notdevelop PCP, including when the patient is HIV-negative. The PCP statusof HIV-negative human patients is especially difficult to determine,because the P. jirovecii charge of these patients is lower than that ofHIV-positive human patients. The means of the application may therebyavoid that said P. jirovecii carriers receive an unnecessary PCPtreatment.

The means of the application involve the detection and/orquantification, more particularly the quantification, of the RNAtranscripts of two different P. jirovecii mitochondrial genes. The meansof the application involve more particularly determining the ratio ofthe RNA transcripts of one of said two different P. jiroveciimitochondrial genes (hereinafter the first P. jirovecii mitochondrialgene) to the RNA transcripts of the other of said two different P.jirovecii mitochondrial genes (hereinafter the second P. jiroveciimitochondrial gene).

Each of the two different P. jirovecii mitochondrial genes areindependently selected from the group consisting of

-   -   the P. jirovecii gene (SEQ ID NO: 3), the sequence of which        codes for the Cytb protein, and    -   the P. jirovecii genes, the respective sequences of which        transcribe into a P. jirovecii ribosomal RNA, such as the        mitochondrial P. jirovecii Large Sub-Unit (mtLSU) gene (SEQ ID        NO: 1) and the mitochondrial P. jirovecii Small Sub-Unit (mtSSU)        gene (SEQ ID NO: 2).

At least one of said two different P. jirovecii mitochondrial genes is aP. jirovecii gene, the sequence of which transcribes into a P. jiroveciiribosomal RNA, such as the mtLSU gene or the mtSSU gene.

More particularly, at least one of said two different P. jiroveciimitochondrial genes is the mtLSU gene.

For example, the first P. jirovecii mitochondrial gene of said ratio isthe P. jirovecii gene, the sequence of which codes for the Cytb protein,or is the mtSSU gene.

For example, the second P. jirovecii mitochondrial gene of said ratio isthe mtSSU gene or the mtLSU gene (while still being different from thefirst P. jirovecii mitochondrial gene of said ratio), more particularlythe mtLSU gene.

For example, the first P. jirovecii mitochondrial gene is the P.jirovecii gene, the sequence of which codes for the Cytb protein, andthe second P. jirovecil mitochondrial gene is a P. jirovecii gene, thesequence of which transcribes into a P. jirovecil ribosomal RNA, such asthe mtLSU gene or the mtSSU gene [ratio Cytb/(mtLSU or mtSSU), moreparticularly ratio Cytb/mtLSU]. For example, the first P. jiroveciimitochondrial gene is the mtSSU gene, and the second P. jiroveciimitochondrial gene is the mtLSU gene [ratio mtSSU/mtLSU].

The means of the application are notably suitable

-   -   for diagnosing or predicting PneumoCystis Pneumonia (PCP), more        particularly for diagnosing or predicting whether a human        patient (more particularly a human patient, who is a        Pneumocystis jirovecii carrier) has or develops PCP, or    -   for determining or predicting the efficacy of a drug or        treatment against PCP in a human patient (more particularly a        human patient, who is a Pneumocystis jirovecii carrier), or    -   for determining whether PCP regresses or has been treated in a        human patient who has been diagnosed to have PCP and who is        receiving or has received a drug or treatment against PCP.

The means of the application comprises methods, products (e.g., primersand/or probes), association(s) or combination(s) of at least two ofthese products, as well as kit(s) and composition(s) comprising at leastone of said products.

The means of the application also comprises solid supports such asmicroarray, nanoarray, chip, onto which at least one of said product isattached, as well as nucleic acid library(ies) which are suitable forthe quantification of a P. jirovecii transcriptome, computer programproduct(s), computer device(s) and kit(s) for use in the treatmentand/or prevention and/or palliation of PCP in a human patient.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Comparison of mLSU quantification thresholds obtained with DNA(Cq mtLSU DNA PCR) or RNA amplification (Cq mtLSU RNA PCR) in BALF ofpatients. The mean loss of Cq is 3.58 (95% CI: 2.68-4.47), correspondingapproximately to about a 10 fold higher expression for RNA.

FIGS. 2A and 2B: ROC curves of mtLSU RNA qPCR (qPCR) and the CYTB/mtLSUratio (PCP Xpress) tests for diagnostic (A, n=41) or diagnostic andfollow-up (B, n=46) samples. Sens, sensitivity; Spec, Specificity; LR,Likelihood ratio.

FIG. 3A. Plot of the mtLSU RNA quantification cycle (Cq) for each mtLSUpositive samples in the different categories of samples. The range ofthreshold that allows the higher likelihood ratio is depicted as adotted line]30.49 to 31.78[. Cleared dots are from patients classifiedin a category but for which the ratio is in favor of the other group ofpatient.

FIG. 3B. Plots of the values of the CYTB/mtLSU ratio for each categoryof patients in samples in which both CYTB and mtLSU RNAs were amplified.PCP samples harbored mostly a CYTB/mtLSU <1.27, whereas non-PCP samples(carriers) or patients treated for a minimum of 15 days (PCP Rx)harbored mostly a CYTB/mtLSU ratio >1.66. Sixteen samples had CYTBunamplified so that the ratio was no calculated. Those samples were frompatients without PCP. The range of threshold that allows the higherlikelihood ratio is depicted as a dotted line]1.27 to 1.66[. Cleareddots are from patients classified in a category but for which the ratiois in favor of the other group of patients.

FIG. 4: ROC curve analysis for the BTUB, HSP70 and CYTB to mtLSU ratios.The higher likelihood ration was obtained with the CYTB/mtLSU ratio.

FIG. 5: mtLSU and mtSSU quantification in BAL fluid samples by PCR.

FIG. 6: analysis of the ROC curves obtained with the PCR (cycle)quantification of mtSSU and of mtLSU (in BAL fluid samples), andobtained with the mtSSU/mtLSU ratio. The maximal Likehood Ratio (LR) ofthe mtSSU/mtLSU ratio is at 10 (for an optimal ratio of 2.7) [whereasthe maximal LR of each of mtLSU and mtSSU quantification alone is at 6].A ratio of 3.1-3.3 would however allow to reach a sensitivity of 100%,and may appear preferable for accurate PCP detection.

FIG. 7: distribution of the mtSSU/mtLSU ratio in the BAL fluid samplesof PCP patients and of P. jirovecii carrier (but non-PCP) patients. Theratio of 2.7 is showed in dashed line.

FIGS. 8A and 8B: distribution of the mtSSU (FIG. 8A on the left) andmtLSU (FIG. 8B on the right) quantification cycles in the BAL fluidsamples of PCP patients and of P. jirovecii carrier (but non-PCP)patients.

DETAILED DESCRIPTION OF THE INVENTION

The present application relates to the subject-matter as defined in theclaims as filed and as herein described.

In the application, unless specified otherwise or unless a contextdictates otherwise, all the terms have their ordinary meaning in therelevant field(s).

The application provides means, which involve the detection and/orquantification, more particularly the quantification, of the RNAtranscripts of two different P. jirovecii mitochondrial genes.

An aspect of the application is that the means of the application arebased on the analysis of RNA transcripts, and not on the analysis ofDNA. A further aspect of the application is that the RNA transcripts ofthe application are those of (P. jirovecii) mitochondrial genes.

The means of the application involve more particularly determining theratio of the RNA transcripts of one of said two different P. jiroveciimitochondrial genes (hereinafter the first P. jirovecii mitochondrialgene) to the RNA transcripts of the other of said two different P.jirovecil mitochondrial genes (hereinafter the second P. jiroveciimitochondrial gene).

Each of the two different P. jirovecii mitochondrial genes areindependently selected from the group consisting of

-   -   the P. jirovecil gene (SEQ ID NO: 3), the sequence of which        codes for the Cytb protein, and    -   the P. jirovecii genes, the respective sequences of which        transcribe into a P. jirovecii ribosomal RNA, such as the        mitochondrial P. jirovecii Large Sub-Unit (mtLSU) gene (SEQ ID        NO: 1) and the mitochondrial P. jirovecii Small Sub-Unit (mtSSU)        gene (SEQ ID NO: 2).

At least one of said two different P. jirovecii mitochondrial genes is aP. jirovecii gene, the sequence of which transcribes into a P. jiroveciiribosomal RNA, such as the mtLSU gene or the mtLSU gene.

According to an aspect of the application, at least one of said twodifferent P. jirovecil mitochondrial genes is the mtLSU gene.

According to an aspect of the application, the first of said two P.jirovecii mitochondrial genes is the P. jirovecii gene, the sequence ofwhich codes for the Cytb protein (SEQ ID NO: 3).

The second of said two P. jirovecii mitochondrial genes is a P.jirovecii gene, the sequence of which transcribes into a P. jiroveciiribosomal RNA, such as the mtLSU gene (SEQ ID NO: 1) or the mtSSU gene(SEQ ID NO: 2), more particularly the mtLSU gene.

According to an aspect of the application, the first of said two P.jirovecii mitochondrial genes is the mtSSU gene.

The second of said two P. jirovecii mitochondrial genes is the mtLSUgene, or the P. jirovecii gene, the sequence of which codes for the Cytbprotein, more particularly the mtLSU gene.

According to an aspect of the application, the first of said two P.jirovecii mitochondrial genes is the mtLSU gene.

The second of said two P. jirovecii mitochondrial genes is the mtSSUgene, or the P. jirovecii gene, the sequence of which codes for the Cytbprotein, more particularly the mtSSU gene.

The means of the application are notably suitable

-   -   for diagnosing or predicting PneumoCystis Pneumonia (PCP), more        particularly for diagnosing or predicting whether a human        patient (more particularly a human patient, who is a        Pneumocystis jirovecii carrier) has or develops PCP, or    -   for determining or predicting the efficacy of a drug or        treatment against PCP in a human patient (more particularly a        human patient, who is a Pneumocystis jirovecii carrier), or    -   for determining whether PCP regresses or has been treated in a        human patient who has been diagnosed to have PCP and who is        receiving or has received a drug or treatment against PCP.

Advantageously, the means of the invention are sufficiently reliable todetermine the PCP status of a human patient, who is HIV-negative, moreparticularly a HIV-negative and immunocompromised human patient. The PCPstatus of HIV-negative human patients is especially difficult todetermine, because the P. jirovecii charge of these patients is lowerthan that of HIV-positive human patients.

The quantification of the RNA transcripts of said two different P.jirovecii mitochondrial genes may be achieved by any means that theskilled person may found appropriate. Nevertheless, the applicationprovides Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR) means,which RT-PCR means can be implemented in real-time.

The application relates to an in vitro method for diagnosing orpredicting PneumoCystis Pneumonia (PCP), more particularly an in vitromethod for diagnosing or predicting whether a human patient (moreparticularly a human patient, who is a Pneumocystis jirovecii carrier)has or develops PCP, wherein said method comprises

-   -   i. in the RNA material of a sample of biological fluid        previously obtained from the respiratory tract of said human        patient, detecting and/or quantifying the (number of or the        concentration of) RNA transcripts of (each of) two different P.        jirovecii mitochondrial genes, more particularly quantifying the        (number of or the concentration of) RNA transcripts of (each of)        two different P. jirovecii mitochondrial genes to obtain a value        of quantification of the RNA transcripts of a first P. jirovecii        mitochondrial gene and a value of quantification of the RNA        transcripts of a second P. jirovecil mitochondrial gene,    -   ii. calculating the ratio of the value of quantification of the        RNA transcripts of said first P. jirovecii mitochondrial gene        of i. to the value of quantification of the RNA transcripts of        said second P. jirovecii mitochondrial gene of i., and    -   iii. comparing the value of the ratio of ii. to a threshold        (numerical) value,        wherein said human patient is diagnosed or predicted to be at        high risk of having or developing PCP or to be at low risk of        having or developing PCP depending on whether the value of the        ratio of ii. is equal to or lower than said threshold value, or        whether the value of the ratio of ii. is higher than said        threshold value.

When the first of said two P. jirovecii mitochondrial genes is the P.jirovecii gene, the sequence of which codes for the Cytb protein (SEQ IDNO: 3) and the second of said two P. jirovecii mitochondrial genes isthe mtLSU or mtSSU gene, more particularly the mtLSU gene, or when thefirst of said two P. jirovecii mitochondrial genes is the mtSSU gene andthe second of said two P. jirovecii mitochondrial genes is the mtLSUgene, said step iii. can be the step of comparing the ratio of ii. to athreshold (numerical) value, wherein, when the value of the ratio of ii.is equal to or lower than (more particularly lower than) said thresholdvalue, said human patient is diagnosed or predicted to be at high riskof having or developing PCP,

wherein, when the value of the ratio of ii. is higher than saidthreshold value, said human patient is diagnosed or predicted to be atlow risk of having or developing PCP.

Of course, inverting the first and second mitochondrial genes in theratio results in accordingly inverting the threshold value and theconclusion that results from the comparison of the ratio to thethreshold value.

Therefore, when the first of said two P. jirovecil mitochondrial genesis the mtLSU gene and the second of said two P. jirovecii mitochondrialgenes is the P. jirovecii gene, the sequence of which codes for the Cytbprotein, or is the mtSSU gene, or when the first of said two P.jirovecii mitochondrial genes is the mtSSU gene and the second of saidtwo P. jirovecii mitochondrial genes is the P. jirovecii gene, thesequence of which codes for the Cytb protein, said step iii. can be thestep of comparing the ratio of ii. to a threshold (numerical) value,wherein, when the value of the ratio of ii. is higher or equal than(more particularly higher than) said threshold value, said human patientis diagnosed or predicted to be at high risk of having or developingPCP,

wherein, when the value of the ratio of ii. is lower than said thresholdvalue, said human patient is diagnosed or predicted to be at low risk ofhaving or developing PCP.

Said threshold value may e.g., have been predetermined by comparing thevalues, or the distribution of the values, that the ratio of the valueof quantification of the RNA transcripts of said first P. jiroveciimitochondrial gene to the value of quantification of the RNA transcriptsof said second P. jirovecil mitochondrial gene takes in reference humancohorts of P. jirovecii carriers, who have been pre-established as afunction of their status of:

-   -   P. jirovecii carriers, who have or develop PCP, or of    -   P. jirovecii carriers, who do not have and do not develop PCP,        in order to classify said human patient into that of those        reference cohorts to which it has the highest probability of        belonging.

The reference human cohort of P. jirovecii carriers, who have or developPCP, and the reference human cohort of P. jirovecii carriers, who do nothave and do not develop PCP, may each e.g., comprise more than 100humans. A human carrier of P. jirovecii is classified in either one ofsaid two reference cohorts by any means that the skilled person may findappropriate. For example, said means may comprise the analysis of theclinical, radiological and biological features (including microscopicaldetection of absence or presence of P. jirovecii) of human individualsby two independent experts, e.g., a pneumologist and an infectiousdisease specialist (cf. examples and Table 1 below), and, for each ofsaid human individuals, the concurrent conclusion of either presence ofPCP (proven, probable or possible PCP, more particularly proven PCP), orof absence of PCP.

The application also relates to an in vitro method for determining orpredicting the efficacy of a drug or treatment against PCP in a humanpatient, who is a Pneumocystis jirovecii carrier and who has beendiagnosed to have or to develop PCP, wherein said method comprises

-   -   quantifying (the number of or the concentration of) RNA        transcripts in the RNA material of a sample of biological fluid        previously obtained from the respiratory tract of said human        patient at a first point in time as well as at a second point in        time, wherein said second point in time is later than said first        point in time, wherein at least one of said first and second        points in time is comprised in a time period during which said        human patient is receiving said drug or treatment, wherein said        RNA transcripts are the (respective) RNA transcripts of two        different P. jirovecii mitochondrial genes, to obtain the value        of quantification of the RNA transcripts of said first P.        jirovecii mitochondrial gene at said first point in time and at        said second point in time as well as the value of quantification        of the RNA transcripts of said second P. jirovecii mitochondrial        gene at said first point in time and at said second point in        time, respectively.    -   calculating the ratio of the value of quantification of the RNA        transcripts of said first P. jirovecii mitochondrial gene to the        value of quantification of RNA transcripts of said second P.        jirovecii mitochondrial gene, to obtain the value of said ratio        at said first point in time as well as its value at said second        point in time, and    -   comparing the value of said ratio at said second point in time        to its value at said first point in time, wherein an increase or        a decrease of the value of said ratio at said second point in        time compared to said first point in time is indicative that        said treatment or drug is or will be efficient to treat or        alleviate PCP in said human patient.

When the first of said two P. jirovecii mitochondrial genes is the P.jirovecii gene, the sequence of which codes for the Cytb protein, andthe second of said two P. jirovecii mitochondrial genes is the mtLSUgene or the mtSSU gene, more particularly the mtLSU gene, or when thefirst of said two P. jirovecii mitochondrial genes is the mtSSU gene andthe second of said two P. jirovecii mitochondrial genes is the mtLSUgene, it is an increase of the value of said ratio at said second pointin time compared to said first point in time that is indicative thatsaid treatment or drug is or will be efficient to treat or alleviate PCPin said human patient. The absence of increase, more particularly adecrease, of the value of said ratio at said second point in timecompared to said first point in time may be or is indicative that saidtreatment or drug is not or will not be efficient to treat or alleviatePCP in said human patient.

Of course, inverting the first and second mitochondrial genes in theratio results in accordingly inverting the threshold value and theconclusion that results from the comparison of the ratio to thethreshold value.

Therefore, when the first of said two P. jirovecii mitochondrial genesis the mtLSU gene and the second of said two P. jirovecii mitochondrialgenes is the P. jirovecii gene, the sequence of which codes for the Cytbprotein, or is the mtSSU gene, or when the first of said two P.jirovecii mitochondrial genes is the mtSSU gene and the second of saidtwo P. jirovecii mitochondrial genes is the P. jirovecii gene, thesequence of which codes for the Cytb protein, it is a decrease of thevalue of said ratio at said second point in time compared to said firstpoint in time that is indicative that said treatment or drug is or willbe efficient to treat or alleviate PCP in said human patient. Theabsence of decrease, more particularly an increase, of the value of saidratio at said second point in time compared to said first point in timemay be or is indicative that said treatment or drug is not or will notbe efficient to treat or alleviate PCP in said human patient.

The application also relates to an in vitro method for determiningwhether PCP regresses or has been treated in a human patient who hasbeen diagnosed to have PCP and who is receiving or has received a drugor treatment against PCP, wherein said method comprises

-   -   quantifying (the number of or the concentration of) RNA        transcripts in the RNA material of a sample of biological fluid        previously obtained from the respiratory tract of said human        patient at a first point in time as well as at a second point in        time, wherein said second point in time is later than said first        point in time, wherein at least one of said first and second        points in time is comprised in a time period during which said        human patient is receiving said drug or treatment, wherein said        RNA transcripts are the (respective) RNA transcripts of two        different P. jirovecii mitochondrial genes, to obtain the value        of quantification of the RNA transcripts of said first P.        jirovecii mitochondrial gene at said first point in time and at        said second point in time as well as the value of quantification        of the RNA transcripts of said second P. jirovecii mitochondrial        gene at said first point in time and at said second point in        time, respectively.    -   calculating the ratio of the value of quantification of the RNA        transcripts of said first P. jirovecii mitochondrial gene to the        value of quantification of RNA transcripts of said second P.        jirovecii mitochondrial gene, to obtain the value of said ratio        at said first point in time as well as its value at said second        point in time, and    -   comparing the value of said ratio at said second point in time        to its value at said first point in time, wherein an increase or        a decrease of the value of said ratio at said second point in        time compared to said first point in time is indicative that PCP        regresses or has been treated in said human patient.

When the first of said two P. jirovecii mitochondrial genes is the P.jirovecii gene, the sequence of which codes for the Cytb protein (SEQ IDNO: 3), and the second of said two P. jirovecii mitochondrial genes isthe mtLSU gene or the mtSSU gene, more particularly the mtLSU gene, orwhen the first of said two P. jirovecii mitochondrial genes is the mtSSUgene and the second of said two P. jirovecii mitochondrial genes is themtLSU gene, it is an increase of the value of said ratio at said secondpoint in time compared to said first point in time that is indicativethat PCP regresses or has been treated in said human patient. Theabsence of increase, more particularly a decrease, of the value of saidratio at said second point in time compared to said first point in timemay be or is indicative that PCP does not regress or does not have beentreated in said human patient.

Of course, inverting the first and second mitochondrial genes in theratio results in accordingly inverting the threshold value and theconclusion that results from the comparison of the ratio to thethreshold value.

Therefore, when the first of said two P. jirovecii mitochondrial genesis the mtLSU gene and the second of said two P. jirovecii mitochondrialgenes is the P. jirovecii gene, the sequence of which codes for the Cytbprotein, or is the mtSSU gene, or when the first of said two P.jirovecii mitochondrial genes is the mtSSU gene and the second first ofsaid two P. jirovecii mitochondrial genes is the P. jirovecii gene, thesequence of which codes for the Cytb protein, it is a decrease of thevalue of said ratio at said second point in time compared to said firstpoint in time that is indicative that PCP regresses or has been treatedin said human patient. The absence of decrease, more particularly anincrease, of the value of said ratio at said second point in timecompared to said first point in time may be or is indicative that PCPdoes not regress or does not have been treated in said human patient.

When the first of said two P. jirovecii mitochondrial genes is the P.jirovecii gene, the sequence of which codes for the Cytb protein, thesecond of said two P. jirovecil mitochondrial genes can e.g., be a P.jirovecii gene, the sequence of which transcribes into a P. jirovecilribosomal RNA, such as the mtLSU gene (SEQ ID NO: 1) or the mtSSU gene(SEQ ID NO: 2), more particularly the mtLSU gene.

When the first of said two P. jirovecii mitochondrial genes is the mtSSUgene, the second of said two P. jirovecii mitochondrial genes can e.g.,be the mtLSU gene.

According to an aspect of the application, said second P. jiroveciiribosomal RNA is the mitochondrial P. jirovecii Large Sub-Unit (mtLSU)gene.

According to an aspect of the application, said first P. jiroveciiribosomal RNA is the P. jirovecii gene, the sequence of which codes forthe Cytb protein, or is the mitochondrial P. jirovecii Small Sub-Unit(mtSSU) gene.

Advantageously, the respective RNA transcripts of said two different P.jirovecil mitochondrial genes are quantified in the RNA material of thesame sample of biological fluid.

The RNA material of said sample of biological fluid can be extractedand/or purified from the sample. RNA extraction means and RNApurification means are known to the person of ordinary skill in the art.For example, RNA extraction means comprise cell lysis reagent(s) and/orbuffer(s). For example, RNA purification means comprise silica membrane.

Advantageously, the RNA material of said sample of biological fluid ispurified by silica membrane filtration of said sample of biologicalfluid.

The means of the application may further comprise a control of nucleicacid extraction and/or purification, more particularly an internalcontrol of nucleic acid extraction and/or purification. Moreparticularly, the means of the application may further comprise acontrol of RNA extraction and/or purification, more particularly aninternal control of RNA extraction and/or purification.

More particularly, the means of the application may further comprise aRNA acting as an internal control of RNA extraction and/or purification,more particularly an artificial or exogenous RNA, more particularly aRNA acting as an Internal Extraction Control RNA (IECR) (cf. the example2 below), or may further comprise a cell which comprises such a RNA(e.g., by genetic engineering).

Said RNA or IECR may e.g., be a RNA sequence (e.g., a RNA sequence of30-500 nucleotides), which is not a human or fungal nucleic acidsequence, more preferably which has less than 60% (e.g., less than 50%,less than 40%, less than 30%, less than 20%, less than 10%, less than1%) identity to any human or fungal nucleic acid sequence. Examples ofIECR are commercially available. Examples of IECR include:

-   -   the RNA extraction control commercialized by BIOLINE (BIOLINE        USA Inc.; 305 Constitution Dr.; TAUNTON; Mass. 027080; U.S.A.)        under catalog number BIO-38040 or BIO-35040,    -   the AMBION® ERCC RNA Spike-In Controls, which are commercialized        by LIFE TECHNOLOGIES S.A.S. (route de l'orme des merisiers;        Immeuble Discovery—Zone Technologique; 91190 SAINT AUBIN,        FRANCE), under catalog number 4456740, and    -   the RNA Internal Control, which is commercialized by QIAGEN®        (QIAGEN® France S.A.S.; 3, avenue du Canada: LP 809; 91974        COURTABOEUF CEDEX; FRANCE) under catalog number 211492.

Alternatively to the IECR, the internal control of RNA extraction and/orpurification can be performed by detecting that a human gene is stillpresent after said extraction and/or purification step. Examples ofsuitable human genes are known in the art and include constitutivegenes, such as the human albumin (ALB) gene or the human TATA Boxbinding protein (TBP). Hence, the means of the application may furthercomprise at least probe, more particularly at least one (real-time)probe and at least one primer pair, which specifically detect a humangene, such as the human albumin (ALB) gene or the human TATA Box bindingprotein (TBP); cf. example 2 below.

Said sample of biological fluid may e.g., be a sample of lowerrespiratory tract fluid, such as a sample of bronchoalveolar lavagefluid, or induced sputum, or a sample of upper respiratory tract fluid,such as a sample of sputum, nasopharyngeal aspirate, oral wash or nasalswab.

Said human patient can be HIV-positive or is HIV-negative, moreparticularly HIV-negative. More particularly, said human patient isHIV-negative and immunocompromised. Advantageously, the means of theapplication are reliable with HIV-negative human patients, whereas theP. jirovecii charge of HIV-negative human patients is lower than that ofHIV-positive human patients.

Advantageously, said human patient is a human patient, more particularlya HIV-negative human patient, who is receiving, has received or willreceive an immunosuppressive treatment, more particularly animmunosuppressor agent or drug, more particularly chemotherapy, anantirejection drug or steroids. For example, said human patient is ahuman patient, more particularly a HIV-negative human patient, who isreceiving, has received or will receive a graft of organ(s) and/ortissue(s) (e.g., bone marrow, heart, kidney, liver organ(s), and/ortissue(s) thereof). Said immunosuppressive treatment, immunosuppressoragent or drug, antirejection drug may e.g., be intended to preventand/or palliate the rejection of said transplanted organ(s) andtissue(s) and/or graft-versus-host disease. For example, said humanpatient is a human patient, more particularly a HIV-negative patient,who has an autoimmune disease and/or an inflammatory disease.

Advantageously, said human patient is a human patient, more particularlya HIV-negative human patient, who has a haematological malignancy and/ora solid malignancy.

Advantageously, said human patient is a human patient, more particularlya HIV-negative human patient, who is a preterm baby (more particularly apreterm baby, who is born at less than 37 weeks gestational age), anewborn or neonate (more particularly of 1-day old to less than 4-weekold) or an infant (more particularly of 4-week old to less than 1-yearold). More particularly, said human patient is a human patient, moreparticularly a HIV-negative human patient, who is a preterm baby (moreparticularly a preterm baby, who is born at less than 37 weeksgestational age), a newborn or neonate (more particularly of 1-day oldto less than 4-week old).

Advantageously, said quantification of RNA transcripts is performed by(cDNA) reverse-transcription and PCR amplification (for each of said twoP. jirovecii mitochondrial genes). More particularly, said (cDNA)reverse-transcription and PCR amplification can be performed (as aone-step RT-PCR reaction, i.e.,) in the same tube (for each of said twoP. jirovecii mitochondrial genes).

Hence, the (cDNA) reverse-transcription and PCR amplification of the RNAtranscripts of said first P. jirovecii mitochondrial gene can beperformed in the same tube, and the reverse-transcription and PCRamplification of the RNA transcripts of said second P. jiroveciimitochondrial gene can be performed in the same tube.

The (cDNA) reverse-transcription and PCR amplification of the RNAtranscripts of said first P. jirovecil mitochondrial gene can beperformed in a tube different from, or in the same tube as, the tube inwhich the (cDNA) reverse-transcription and PCR amplification of the RNAtranscripts of second first P. jirovecii mitochondrial gene isperformed.

Said PCR advantageously is real-time PCR.

Advantageously, said PCR is a quantitative PCR, more particularly aquantitative real-time PCR, more particularly a quantitative real-timeRT-PCR, more particularly a one-step quantitative real-time RT-PCR.

Said threshold value can e.g., be in the 1.00-2.00 range, moreparticularly in the 1.00-1.80 range, more particularly in the 1.20-1.70range, more particularly in the 1.27-1.66 range, more particularly is of1.50.

For example, said ratio calculation is performed using the equation

R=E(CYTb)^(−Cq(CYTb)) /E(mtrDNA)^(−Cq(mtrDNA))

wherein

-   -   R is said ratio,    -   CYTB is the cDNA reverse-transcript of the RNA transcripts of        said P. jirovecii gene, the sequence of which codes for the Cytb        protein,    -   mtrDNA is the cDNA reverse-transcript of the RNA transcripts of        said P. jirovecii gene, the sequence of which transcribes into        a P. jirovecii ribosomal RNA,    -   E is the value of the PCR efficiency of one amplification cycle        in the exponential phase for the indicated cDNA, and    -   Cq is the value of the PCR quantification cycle for the        indicated cDNA.

Advantageously, said ratio is the fold change of the value ofquantification of the RNA transcripts of said first P. jiroveciimitochondrial gene compared to said second P. jirovecii mitochondrialgene.

These features may notably apply when said first P. jiroveciimitochondrial gene is the P. jirovecii gene, the sequence of which codesfor the Cytb protein, and when said second P. jirovecil mitochondrialgene is a P. jirovecii gene, the sequence of which transcribes into a P.jirovecii ribosomal RNA, such as the mtLSU gene or the mtSSU gene, moreparticularly the mtLSU gene.

Of course, when said first P. jirovecil mitochondrial gene is the mtLSUgene and said second P. jirovecii mitochondrial gene is the P. jiroveciigene, the sequence of which codes for the Cytb protein, said thresholdvalue can e.g., be in the 1/2.00-1/1.00 range, more particularly in the1/1.80-1/1.00 range, more particularly in the 1/1.70-1/1.20 range, moreparticularly in the 1/1.66-1/1.27 range, more particularly is of 1/1.50.

Said threshold value can e.g., be in the 2.7-3.3 range, moreparticularly in the 3.1-3.3 range, for example 3.2.

For example, the ratio calculation is performed using the equation

R=E(mtSSU)^(−Cq(mtSSU)) /E(mtLSU)^(−Cq(mtLSU))

wherein

-   -   R is said ratio,    -   mtSSU is the cDNA reverse-transcript of the RNA transcripts of        said mitochondrial P. jirovecii mtSSU gene,    -   mtLSU is the cDNA reverse-transcript of the RNA transcripts of        said mitochondrial P. jirovecii mtLSU gene,    -   E is the value of the PCR efficiency of one amplification cycle        in the exponential phase for the indicated cDNA, and    -   Cq is the value of the PCR quantification cycle for the        indicated cDNA.

These features may notably apply when said first P. jirovecilmitochondrial gene is the mtSSU gene, and wherein said second P.jirovecii mitochondrial gene is the mtLSU gene.

Of course, when said first P. jirovecil mitochondrial gene is the mtLSUgene and said second P. jirovecii mitochondrial gene is the mtSSU gene,said threshold value can e.g., be in the 1/3.3-1/2.7 range, moreparticularly in the 1/3.3-1/3.1 range, for example 1/3.2.

In a method of the application, the quantification of the respective RNAtranscripts may be achieved by any means that the person of ordinaryskill in the art may found appropriate.

Such means include hybridization- or sequence-based means, as well asany means that enable to quantify a transcriptome, such as e.g., theRNA-Seq method (cf. Wang et al. 2009). The application provides a DNAlibrary as well as computer means, which are suitable for implementationof the RNA-Seq method (cf. below).

In a method of the application, the quantification of the respective RNAtranscripts may comprise:

-   -   the cDNA reverse transcription of the RNA transcripts of said        first P. jirovecii mitochondrial gene (using a reverse        transcriptase) to obtain first cDNA reverse-transcripts, and the        PCR amplification of a first cDNA target from said first cDNA        reverse-transcripts (using a polymerase and) using a first        primer pair to obtain first amplicons (first cDNA or DNA nucleic        acids), and    -   the cDNA reverse transcription of the RNA transcripts of said        second P. jirovecii mitochondrial gene (using a reverse        transcriptase and) to obtain second cDNA reverse-transcripts,        and the PCR amplification of a second cDNA target from said        second cDNA reverse-transcripts (using a polymerase and) using a        second primer pair to obtain second amplicons (second cDNA or        DNA nucleic acids),        wherein said method further comprises the quantification of (the        number of or the concentration of) said first amplicons and of        (the number of or the concentration of) said second amplicons,        wherein the value of quantification of (e.g., the number of or        the concentration of) said first amplicons is the value of        quantification of (e.g., the number of or the concentration of)        the RNA transcripts of said first P. jirovecii mitochondrial        gene, and the value of quantification of (e.g., the number of or        the concentration of) said second amplicons is the value of        quantification of (e.g., the number of or the concentration of)        the RNA transcripts of said second P. jirovecii mitochondrial        gene.

When said first P. jirovecii mitochondrial gene is the P. jiroveciigene, the sequence of which codes for the Cytb protein, said first cDNAtarget advantageously consists of 100-120 nucleotides (more particularlyof 100-110 nucleotides, more particularly of 102-108 nucleotides, moreparticularly of 104-106 nucleotides, more particularly of 105nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 30, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 30        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID NO:        30.

When said first P. jirovecii mitochondrial gene is the mtSSU gene, saidfirst cDNA target advantageously consists of 60-110 nucleotides andcomprises or is

-   -   the sequence of SEQ ID NO: 15 or of SEQ ID NO: 20 or of SEQ ID        NO: 25, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 15 or        as SEQ ID NO: 20 or as SEQ ID NO: 25, and which is at least 95%        identical to SEQ ID NO: 15 or SEQ ID NO: 20 or SEQ ID NO: 25,        respectively.

When said second P. jirovecii mitochondrial gene is mtLSU gene, saidsecond cDNA target advantageously consists of 115-125 nucleotides andcomprises or is

-   -   the sequence of SEQ ID NO: 10, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 10        and which is at least 95% identical to SEQ ID NO: 10.

When said second P. jirovecii mitochondrial gene is the P. jiroveciigene is the mtSSU gene, said second cDNA target advantageously consistsof 60-110 nucleotides and comprises or is

-   -   the sequence of SEQ ID NO: 15 or of SEQ ID NO: 20 or of SEQ ID        NO: 25, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 15 or        as SEQ ID NO: 20 or as SEQ ID NO: 25, and which is at least 95%        identical to SEQ ID NO: 15 or SEQ ID NO: 20 or SEQ ID NO: 25,        respectively.

In a method of the application, the quantification of the respective RNAtranscripts comprises:

-   -   the cDNA reverse transcription of a first RNA target contained        in the RNA transcripts of said first P. jirovecii mitochondrial        gene (using a reverse transcriptase and) using a first primer        pair to obtain first cDNA reverse-transcripts, and the PCR        amplification of said first cDNA reverse-transcripts (using a        polymerase and) using the same first primer pair to obtain first        amplicons, and    -   the cDNA reverse transcription of a second RNA target from the        RNA transcripts of said second P. jirovecii mitochondrial gene        (using a reverse transcriptase and) using a second primer pair        to obtain second cDNA reverse-transcripts, and the PCR        amplification of said second cDNA reverse-transcripts (using a        polymerase and) using the same second primer pair to obtain        second amplicons.        wherein said method further comprises the quantification of (the        number of or the concentration of) said first amplicons and of        (the number of or the concentration of) said second amplicons,        wherein the value of quantification of (e.g., the number of or        the concentration of) said first amplicons is the value of        quantification of (e.g., the number of or the concentration of)        the RNA transcripts of said first P. jirovecil mitochondrial        gene, and the value of quantification of (e.g., the number of or        the concentration of) said second amplicons is the value of        quantification of (e.g., the number of or the concentration of)        the RNA transcripts of said second P. jirovecii mitochondrial        gene.

When said first P. jirovecii mitochondrial gene is the P. jiroveciigene, the sequence of which codes for the Cytb protein, said first RNAtarget may advantageously consist of 100-120 nucleotides (moreparticularly of 100-110 nucleotides, more particularly of 102-108nucleotides, more particularly of 104-106 nucleotides, more particularlyof 105 nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 29, or    -   a RNA sequence, which is of the same length as SEQ ID NO: 29 and        which is at least 95% (more particularly at least 96%, at least        97%, at least 98% or at least 99%) identical to SEQ ID NO: 29.

When said first P. jirovecii mitochondrial gene is the mrSSU gene, saidfirst RNA target advantageously consists of 60-110 nucleotides andcomprises or is

-   -   the sequence of SEQ ID NO: 14 or of SEQ ID NO: 19 or of SEQ ID        NO: 24, or    -   a RNA sequence, which is of the same length as SEQ ID NO: 14 or        as SEQ ID NO: 19 or as SEQ ID NO: 24, and which is at least 95%        identical to SEQ ID NO: 14 or SEQ ID NO: 19 or SEQ ID NO: 24,        respectively.

When said second P. jirovecii mitochondrial gene is the mtLSU gene, saidsecond RNA target advantageously consists of 115-125 nucleotides andcomprises or is

-   -   the sequence of SEQ ID NO: 9, or    -   a RNA sequence, which is of the same length as SEQ ID NO: 9 and        which is at least 95% identical to SEQ ID NO: 9.

When said second P. jirovecil mitochondrial gene is the mtSSU gene, saidsecond RNA target advantageously consists of 60-110 nucleotides andcomprises or is

-   -   the sequence of SEQ ID NO: 14 or of SEQ ID NO: 19 or of SEQ ID        NO: 24, or    -   a RNA sequence, which is of the same length as SEQ ID NO: 14 or        as SEQ ID NO: 19 or as SEQ ID NO: 24, and which is at least 95%        identical to SEQ ID NO: 14 or SEQ ID NO: 19 or SEQ ID NO: 24,        respectively.

In the application, and in accordance with the understanding of theperson of average skill in the art, the phrase “reverse polymerase”refers to a RNA-dependent DNA polymerase, and the phrase “polymerase”refers to a “DNA-dependent DNA polymerase”.

The term “nucleotide” encompasses naturally-occurring nucleotides, aswell as no-naturally-occurring nucleotides, such as Locked Nucleic Acid(LNA™) nucleotides. A LNA™ nucleotide is understood in accordance withits ordinary meaning in the field, i.e., a nucleotide in which theribose or deoxyribose ring is “locked” by a methylene bridge connectingthe 2′-O atom and the 4′-C atom. The term “nucleotide” encompasses moreparticularly naturally-occurring nucleotides (nucleotides A, G, T and Cfor DNA molecules; nucleotides A, G, U and C for RNA molecules).

In other words, when said first or second P. jirovecii mitochondrialgene is the P. jirovecii gene, the sequence of which codes for the Cytbprotein, said first or second primer pair is a primer pair which annealsto the cDNA reverse transcripts of the RNA transcripts of said first orsecond P. jirovecii mitochondrial gene (or to the RNA transcripts ofsaid first or second P. jirovecii mitochondrial gene as well as to thecDNA reverse transcripts thereof) respectively, to produce a (cDNA orDNA) amplicon (or to produce cDNA reverse-transcripts as well as the(cDNA or DNA) amplicon thereof), which is of 100-120 nucleotide-long(more particularly of 100-110 nucleotide-long, more particularly of102-108 nucleotide-long, more particularly of 104-106 nucleotide-long,more particularly of 105 nucleotide-long), and which comprises or is

-   -   the sequence of SEQ ID NO: 30, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 30        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID NO:        30.

The nucleotide sequence of each primer of said first or second primerpair may independently consist of 15-30 nucleotides (more particularlyof 18-28 nucleotides, more particularly of 19-27 nucleotides, moreparticularly of 20-26 nucleotides, more particularly of 20 nucleotides).

For example, said first or second primer pair is the primer pair of SEQID NO: 31 and SEQ ID NO: 32. Alternatively, said first or second primerpair is the primer pair of SEQ ID NO: 60 and SEQ ID NO: 32.

Said first or second cDNA or RNA target may be a P. jirovecii mtLSUtarget.

For example, when said first or second P. jirovecii mitochondrial geneis the mtLSU gene, said first or second (mtLSU) cDNA target may consistof 115-125 nucleotides (more particularly of 117-124 nucleotides, moreparticularly of 119-123 nucleotides, more particularly of 121nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 10, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 10        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID NO:        10.

For example, said first or second (mtLSU) RNA target may consist of115-125 nucleotides (more particularly of 117-124 nucleotides, moreparticularly of 119-123 nucleotides, more particularly of 121nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 9, or    -   a RNA sequence, which is of the same length as SEQ ID NO: 9 and        which is at least 95% (more particularly at least 96%, at least        97%, at least 98% or at least 99%) identical to SEQ ID NO: 9.

In other words, said first or second primer pair may e.g., be a (mtLSU)primer pair, which anneals to the cDNA reverse-transcripts of the RNAtranscripts of the P. jirovecil mtLSU gene (or to the RNA transcripts ofthe P. jirovecii mtLSU gene as well as to the cDNA reverse-transcriptsthereof) to produce a (cDNA or DNA) amplicon (or to produce cDNAreverse-transcripts as well as the (cDNA or DNA) amplicon thereof),which is of 115-125 nucleotides (more particularly of 117-124nucleotides, more particularly of 119-123 nucleotides, more particularlyof 121 nucleotides), and which comprises or is

-   -   the sequence of SEQ ID NO: 10, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 10        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID NO:        10.

The nucleotide sequence of each (mtLSU) primer of first or said secondprimer pair may independently consist of 15-30 nucleotides (moreparticularly of 18-28 nucleotides, more particularly of 19-27nucleotides, more particularly of 20-26 nucleotides, more particularlyof 26 nucleotides).

For example, said first or second primer pair is the (mtLSU) primer pairof SEQ ID NO: 11 and SEQ ID NO: 12.

Alternatively, said first or second cDNA or RNA target may e.g., be a P.jirovecii mtSSU target.

For example, said first or second (mtSSU) cDNA target may consist of60-110 nucleotides (more particularly of 76-92 nucleotides, moreparticularly of 76, 82 or 92 nucleotides, more particularly of 82nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 15, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 15        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID NO:        15.

For example, said first or second (mtSSU) RNA target may consist of60-110 nucleotides (more particularly of 76-92 nucleotides, moreparticularly of 76, 82 or 92 nucleotides, more particularly of 82nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 14, or    -   a RNA sequence, which is of the same length as SEQ ID NO: 14 and        which is at least 95% (more particularly at least 96%, at least        97%, at least 98% or at least 99%) identical to SEQ ID NO: 14.

In other words, said first or second primer pair may alternatively be a(mtSSU) primer pair, which anneals to the cDNA reverse transcripts ofthe RNA transcripts of the P. jirovecii mtSSU gene (or to the RNAtranscripts of the P. jirovecii mtSSU gene as well as to the cDNAreverse transcripts thereof) to produce a (cDNA or DNA) amplicon (or toproduce cDNA reverse-transcripts as well as the (cDNA or DNA) ampliconthereof), which is of 60-110 nucleotides (more particularly of 76-92nucleotides, more particularly of 76, 82 or 92 nucleotides, moreparticularly of 82 nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 15, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 15        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID NO:        15.

The nucleotide sequence of each (mtSSU) primer of said first or secondprimer pair may independently consist of 15-30 nucleotides (moreparticularly of 18-28 nucleotides, more particularly of 19-27nucleotides, more particularly of 20-26 nucleotides, more particularlyof 20-23 nucleotides).

For example, said first or second primer pair is the (mtSSU) primer pairof SEQ ID NO: 16 and SEQ ID NO: 17.

For example, said first or second (mtSSU) cDNA target may consist of60-110 nucleotides (more particularly of 76-92 nucleotides, moreparticularly of 76, 82 or 92 nucleotides, more particularly of 92nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 20, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 20        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID NO:        20.

For example, said first or second (mtSSU) RNA target may consist of60-110 nucleotides (more particularly of 76-92 nucleotides, moreparticularly of 76, 82 or 92 nucleotides, more particularly of 92nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 19, or    -   a RNA sequence, which is of the same length as SEQ ID NO: 19 and        which is at least 95% (more particularly at least 96%, at least        97%, at least 98% or at least 99%) identical to SEQ ID NO: 19.

In other words, said first or second primer pair may alternatively be a(mtSSU) primer pair, which anneals to the cDNA reverse transcripts ofthe RNA transcripts of the P. jirovecii mtSSU gene (or to the RNAtranscripts of the P. jirovecii mtSSU gene as well as to the cDNAreverse transcripts thereof) to produce a (cDNA or DNA) amplicon (or toproduce cDNA reverse-transcripts as well as the (cDNA or DNA) ampliconthereof), which is of 60-110 nucleotides (more particularly of 76-92nucleotides, more particularly of 76, 82 or 92 nucleotides, moreparticularly of 92 nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 20, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 20        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID NO:        20.

The nucleotide sequence of each (mtSSU) primer of said first or secondprimer pair may independently consist of 15-30 nucleotides (moreparticularly of 18-28 nucleotides, more particularly of 19-27nucleotides, more particularly of 20-26 nucleotides, more particularlyof 20-23 nucleotides).

For example, said first or second primer pair is the (mtSSU) primer pairof SEQ ID NO: 21 and SEQ ID NO: 22.

For example, said first or second (mtSSU) cDNA target may consist of60-110 nucleotides (more particularly of 76-92 nucleotides, moreparticularly of 76, 82 or 92 nucleotides, more particularly of 76nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 25, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 25        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID NO;        25.

For example, said first or second (mtSSU) RNA target may consist of60-110 nucleotides (more particularly of 76-92 nucleotides, moreparticularly of 76, 82 or 92 nucleotides, more particularly of 76nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 24, or    -   a RNA sequence, which is of the same length as SEQ ID NO: 24 and        which is at least 95% (more particularly at least 96%, at least        97%, at least 98% or at least 99%) identical to SEQ ID NO; 24.

In other words, said first or second primer pair may alternatively be a(mtSSU) primer pair, which anneals to the cDNA reverse transcripts ofthe RNA transcripts of the P. jirovecii mtSSU gene (or to the RNAtranscripts of the P. jirovecii mtSSU gene as well as to the cDNAreverse transcripts thereof) to produce a (cDNA or DNA) amplicon (or toproduce cDNA reverse-transcripts as well as the (cDNA or DNA) ampliconthereof), which is of 60-110 nucleotides (more particularly of 76-92nucleotides, more particularly of 76, 82 or 92 nucleotides, moreparticularly of 76 nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 25, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 25        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID NO:        25.

The nucleotide sequence of each (mtSSU) primer of said first or secondprimer pair may independently consist of 15-30 nucleotides (moreparticularly of 18-28 nucleotides, more particularly of 19-27nucleotides, more particularly of 20-26 nucleotides, more particularlyof 20-23 nucleotides).

For example, said first or second primer pair is the (mtSSU) primer pairof SEQ ID NO: 26 and SEQ ID NO: 27.

Advantageously, the Tm of said first primer pair does not differ by morethan 5° C. (more particularly by more than 4° C., more particularly bymore than 3° C., more particularly by more than 2° C., more particularlyby more than 1° C.) from the Tm of said second primer pair. The Tm ofsaid first primer pair may be identical to the Tm of said second primerpair.

Alternatively or complementarily, the Tm of said first primer pair andthe Tm of said second primer pair may both be of 53° C. or above. Moreparticularly, said first primer pair and said second primer pair mayboth have a Tm in the 53-65° C. range (more particularly in the 56-64°C. range, more particularly in the 57-63° C. range, more particularly inthe 58-63° C. range, more particularly in the 59-62° C. range, moreparticularly in the 59-61° C. range). For example, said first primerpair and said second primer pair may both have a Tm of 60° C.

For example, the Tm of said first primer pair and the Tm of said secondprimer pair are both in the 58-63° C. range and do not differ by morethan 5° C. from each other.

Any PCR or RT-PCR conditions that the skilled person finds appropriatemay be implemented.

For example, the PCR amplification (for each of said first and second P.jirovecii mitochondrial genes) comprises:

-   -   polymerase activation at 95° C. for 2-10 min, and    -   45-50 cycles of 95° C. for 15-30 seconds and 60° C. for 30-60        seconds.

For example, the PCR amplification (for each of said first and second P.jirovecil mitochondrial genes) comprises:

-   -   polymerase activation at 95° C. for 2 min, and    -   45 cycles of 95° C. for 15 seconds and 60° C. for 30 seconds.

For example, the RT-PCR amplification comprises (for each of said firstand second P. jirovecii mitochondrial genes):

-   -   reverse transcription at 42-61° C., preferably 50° C. for 2-15        min,    -   polymerase activation at 95° C. for 2 min, and    -   45 cycles of 95° C. for 15 seconds and 60° C. for 30 seconds.

For example, the RT-PCR amplification comprises (for each of said firstand second P. jirovecii mitochondrial genes):

-   -   reverse transcription at 50° C. for 2 min,    -   polymerase activation at 95° C. for 2 min, and    -   45 cycles of 95° C. for 15 seconds and 60° C. for 30 seconds.

The quantification of the RNA transcripts of said first and/or (moreparticularly, and) said second P. jirovecii mitochondrial gene can beperformed using probes, more particularly

-   -   using at least one first probe, which hybridizes to the cDNA        reverse-transcript of said first P. jirovecii mitochondrial gene        (CYTB), and/or (more particularly, and) at least one second        probe, which hybridizes to the cDNA reverse-transcript of said        second P. jirovecii mitochondrial gene (mtLSU or mtSSU, more        particularly mtLSU), or more particularly    -   using at least one first probe, which hybridizes to the cDNA        reverse-transcript of said first P. jirovecii mitochondrial gene        (mtSSU), and/or (more particularly, and) at least one second        probe, which hybridizes to the cDNA reverse-transcript of said        second P. jirovecii mitochondrial gene (mtLSU).

Each of said first and second probes may independently consist of 17-37nucleotides.

More particularly, the quantification of the RNA transcripts of saidfirst P. jirovecii mitochondrial gene can be performed using at leastone first probe, which hybridizes to said first cDNA target (or saidfirst amplicons), without hybridizing to said second cDNA target (or tosaid second amplicons).

More particularly, the quantification of the RNA transcripts of saidfirst P. jirovecii mitochondrial gene can be performed using at leastone first probe, which specifically hybridizes to said first cDNA target(or to said first amplicons).

More particularly, the quantification of the RNA transcripts of saidsecond P. jirovecil mitochondrial gene can be performed using at leastone second probe, which hybridizes to said second cDNA target (or saidsecond amplicons), without hybridizing to said first cDNA target (or tosaid first amplicons).

More particularly, the quantification of the RNA transcripts of saidsecond P. jirovecii mitochondrial gene can be performed using at leastone second probe, which specifically hybridizes to said second cDNAtarget (or to said second amplicons).

The quantification of the RNA transcripts of said first P. jiroveciimitochondrial gene may e.g., be performed using (at least one) firstprobe, which hybridizes to the cDNA reverse-transcript of said first P.jirovecii mitochondrial gene.

For example, when said first P. jirovecii mitochondrial gene is the P.jirovecii gene, the sequence of which codes for the Cytb protein, saidfirst probe may hybridize to the sequence of SEQ ID NO: 3 or thecomplementary sequence thereof, more particularly to the sequence of SEQID NO: 30 or the complementary sequence thereof, without hybridizing toany of SEQ ID NO: 1 (P. jirovecii mtLSU gene) and the sequencecomplementary to SEQ ID NO: 1, or to any of SEQ ID NO: 2 (P. jiroveciimtSSU gene) and the sequence complementary to SEQ ID NO: 2, moreparticularly to any of SEQ ID NO: 1, the sequence complementary to SEQID NO: 1. SEQ ID NO: 2 and the sequence complementary to SEQ ID NO: 2.Said first probe may also not hybridize to human DNA or RNA.Advantageously, said first probe specifically hybridizes to the sequenceof SEQ ID NO: 3 or the complementary sequence thereof, more particularlyto the sequence of SEQ ID NO: 30 or the complementary sequence thereof.

The sequence of said first probe may e.g., consist of or comprise ahybridization portion, which is or acts as the hybridization portion ofthe probe, i.e., which is or acts as the DNA or RNA portion, whichconfers to the first probe the capacity to hybridize to the cDNAreverse-transcript of said first P. jirovecii mitochondrial gene.

Said hybridization portion may e.g., be a DNA or RNA sequence of 19-30nucleotides (more particularly of 20-24 nucleotides, more particularlyof 22 nucleotides), which hybridizes to the sequence of SEQ ID NO: 3 orthe sequence complementary to SEQ ID NO: 3, more particularly to thesequence of SEQ ID NO: 30 or the sequence complementary to SEQ ID NO:30, without hybridizing to any of SEQ ID NO: 1 and the sequencecomplementary to SEQ ID NO: 1, or to any of SEQ ID NO: 2 and thesequence complementary to SEQ ID NO: 2, more particularly to any of SEQID NO: 1, the sequence complementary to SEQ ID NO: 1, SEQ ID NO: 2 andthe sequence complementary to SEQ ID NO: 2. Said hybridization portionof said first probe may also not hybridize to human DNA or RNA. Saidhybridization portion of said first probe may specifically hybridize tothe sequence of SEQ ID NO: 3 or to the complementary sequence thereof,more particularly to the sequence of SEQ ID NO: 30 or to thecomplementary sequence thereof. For example, the hybridization portionof said first probe is the (22 nucleotide-long) sequence of SEQ ID NO:33 or the complementary sequence thereof, or a LNA-counterpart thereof,such as the (22 nucleotide-long) sequence of SEQ ID NO: 58 or thecomplementary sequence thereof (SEQ ID NO: 59; cf. example 3 below).

The sequence of said first probe may consist of said hybridizationportion.

Alternatively, the sequence of said first probe may comprise other DNAor RNA sequence(s) in addition to said hybridization portion, e.g.,other DNA or RNA sequence(s) linked to the 5′ and/or 3′ terminal end(s)of said hybridization portion. This (these) other DNA or RNA sequence(s)should not (significantly) reduce the hybridization specificity of saidhybridization portion. Said other DNA or RNA sequence(s) may e.g., bebeacon arm(s), more particularly a 5′ beacon arm and a 3′ beacon arm,which impart a hairpin-configuration to said first probe whenunhybridized (e.g., the 3′ beacon arm is complementary to the 5′ beaconarm). The total length of said first probe advantageously is of 28-32nucleotides, or of 27-31 nucleotides, or of 26-30 nucleotides, or of25-29 nucleotides.

Said first probe may comprise (e.g., be covalently linked to) at leastone fluorophore (e.g., 6-carboxyfluorescein, or tetrachlorofluorescein)and/or at least one quencher (e.g., a carboxytetramethylrhodaminefluorescent dye (e.g., TAMRA®), the Black Hole Quencher®-0, the BlackHole Quencher®-1, the Black Hole Quencher®-2, the Black HoleQuencher®-3, or the Minor Groove Binder® quencher).

Said first probe may e.g., be a Locked Nucleic Acid (LNA) probe.

Said first probe may e.g., be a DNA or RNA probe. For example, saidfirst probe may be a TAQMAN® probe, i.e., a probe, wherein a fluorophoreis covalently attached to its 5′-end and a quencher is covalentlyattached to its at the 3′-end (e.g., TAMRA® or BHQ®-1). A TAQMAN® probeis degraded by the 5′-3′ exonuclease activity of the PCR polymerase,thereby releasing the fluorophore from it (and from the proximity of thequencher).

Alternatively, said first probe may be a beacon probe, i.e., a probewhich in addition to said hybridization portion, comprises a beacon armlinked to the 5′ terminal end and a beacon arm linked to the 3′ terminalend (which impart a hairpin-configuration to said first probe whenunhybridized), and which carries a fluorophore covalently linked to oneof said two beacon arms, and a quencher linked to the other of said twobeacon arms.

Alternatively, said first probe may be a SCORPION® probe (i.e., a probe,which is linked to a fluorophore at one of its ends and which is linkedat the other end to a primer via a PCR blocker).

The quantification may also be performed using at least two of saidfirst probes (i.e., two different first probes) each comprising at leastone fluorophore (e.g., as LIGHTCYCLER® hybridization probes).

The Tm of the probe may be 4-10° C. higher than the Tm of the primerpair.

For example, when said first P. jirovecii mitochondrial gene is themtSSU gene, said first probe may hybridize to

-   -   the P. jirovecil mtSSU gene, which is of SEQ ID NO: 2 or to the        sequence complementary to SEQ ID NO: 2, more particularly to the        sequence of SEQ ID NO: 15 (a P. jirovecii mtLSU target) or to        the sequence complementary to SEQ ID NO: 15, and/or    -   to the sequence of SEQ ID NO: 20 (another P. jirovecii mtLSU        target) or to the sequence complementary to SEQ ID NO: 20,        and/or    -   to the sequence of SEQ ID NO: 25 (still another P. jirovecii        mtLSU target) or to the sequence complementary to SEQ ID NO: 25.

More particularly, said first probe may hybridize to the sequence of SEQID NO: 2 or the complementary sequence thereof, more particularly to atleast one of the sequences of SEQ ID NO: 15, 20, 25 and thecomplementary sequences thereof, without hybridizing to any of SEQ IDNO: 3 (P. jirovecii CYTB gene) and the sequence complementary to SEQ IDNO: 3, or to any of SEQ ID NO: 1 (P. jirovecii mtLSU gene) and thesequence complementary to SEQ ID NO: 1, more particularly withouthybridizing to any of SEQ ID NO: 3, the sequence complementary to SEQ IDNO: 3, SEQ ID NO: 1 and the sequence complementary to SEQ ID NO: 1.

Said first probe may also not hybridize to human DNA or RNA.

Advantageously, said first probe specifically hybridizes to the sequenceof SEQ ID NO: 2 or the complementary sequence thereof, more particularlyto at least one of the sequences of SEQ ID NO: 15, 20, 25 and thecomplementary sequences thereof.

The sequence of said first probe may e.g., consist of or comprise ahybridization portion, which is or acts as the hybridization portion ofthe probe, i.e., which is or acts as the DNA portion, which confers tothe first probe the capacity to hybridize to the cDNA reverse-transcriptof said first P. jirovecii mitochondrial gene.

Said hybridization portion may e.g., be a DNA sequence of 23-29nucleotides (more particularly of 25-27 nucleotides), which hybridizesto the sequence of SEQ ID NO: 2 or the sequence complementary to SEQ IDNO: 2, more particularly to at least one of the sequences of SEQ ID NO:15, 20, 25 and the sequences complementary to SEQ ID NO: 10, 20, 25,without hybridizing to any of SEQ ID NO: 3 and the sequencecomplementary to SEQ ID NO: 3, or to any of SEQ ID NO: 1 and thesequence complementary to SEQ ID NO: 1, more particularly withouthybridizing to any of SEQ ID NO: 3, the sequence complementary to SEQ IDNO: 3, SEQ ID NO: 1 and the sequence complementary to SEQ ID NO: 1.

Said hybridization portion of said first probe may also not hybridize tohuman DNA or RNA.

Said hybridization portion of said first probe may specificallyhybridize to the sequence of SEQ ID NO: 2 or to the complementarysequence thereof, more particularly to at least one of the sequences ofSEQ ID NO: 15, 20, 25 and the complementary sequences thereof. Forexample, the hybridization portion of said first probe is the (25 or 27nucleotide-long) sequence of SEQ ID NO: 18, 23 or 28 or thecomplementary sequence thereof.

The sequence of said first probe may consist of said hybridizationportion.

Alternatively, the sequence of said first probe may comprise other DNAsequence(s) in addition to said hybridization portion, e.g., other DNAsequence(s) linked to the 5′ and/or 3′ terminal end(s) of saidhybridization portion. This (these) other DNA sequence(s) should not(significantly) reduce the hybridization specificity of saidhybridization portion. Said other DNA sequence(s) may e.g., be beaconarm(s), more particularly a 5′ beacon arm and a 3′ beacon arm, whichimpart a hairpin-configuration to said first probe when unhybridized(e.g., the 3′ beacon arm is complementary to the 5′ beacon arm). Thetotal length of said first probe advantageously is of 31-37 nucleotides,or of 30-36 nucleotides, or of 29-36 nucleotides, or of 28-34nucleotides.

Said first probe may comprise at least one fluorophore (e.g.,6-carboxyfluorescein, or tetrachlorofluorescein) and/or at least onequencher (e.g., a carboxytetramethylrhodamine fluorescent dye (e.g.,TAMRA®), the Black Hole Quencher®-0, the Black Hole Quencher®-1, theBlack Hole Quencher®-2, the Black Hole Quencher®-3, or the Minor GrooveBinder® quencher).

Said first probe may be a TAQMAN® probe, i.e., a probe, wherein afluorophore is covalently attached to its 5′-end and a quencher iscovalently attached to its at the 3′-end (e.g., TAMRA® or BHQ®-1). ATAQMAN® probe is degraded by the 5′-3′ exonuclease activity of the PCRpolymerase, thereby releasing the fluorophore from it (and from theproximity of the quencher).

Alternatively, said first probe may be a beacon probe, i.e., a probewhich in addition to said hybridization portion, comprises a beacon armlinked to the 5′ terminal end and a beacon arm linked to the 3′ terminalend (which impart a hairpin-configuration to said second probe whenunhybridized), and which carries a fluorophore covalently linked to oneof said two beacon arms, and a quencher linked to the other of said twobeacon arms.

The Tm of the probe may be 4-10° C. higher than the Tm of the primerpair.

When said first P. jirovecii mitochondrial gene is the mtLSU gene, saidfirst probe may hybridize to the P. jirovecii mtLSU gene, which is ofSEQ ID NO: 1 or to the sequence complementary to SEQ ID NO: 1, moreparticularly to the sequence of SEQ ID NO: 10 (a P. jirovecii mtLSUtarget) or to the sequence complementary to SEQ ID NO: 10.

More particularly, said first probe may hybridize to the sequence of SEQID NO: 1 or the complementary sequence thereof, more particularly to thesequence of SEQ ID NO: 10 or the complementary sequence thereof, withouthybridizing to any of SEQ ID NO: 3 (P. jirovecii CYTB gene) and thesequence complementary to SEQ ID NO: 3 or, to any of SEQ ID NO: 2 (P.jirovecii mtSSU gene) and the sequence complementary to SEQ ID NO: 2,more particularly without hybridizing to any of SEQ ID NO: 3, thesequence complementary to SEQ ID NO: 3, SEQ ID NO: 2 and the sequencecomplementary to SEQ ID NO: 2.

Said first probe may also not hybridize to human DNA or RNA.

Advantageously, said first probe specifically hybridizes to the sequenceof SEQ ID NO: 1 or the complementary sequence thereof, more particularlyto the sequence of SEQ ID NO: 10 or the complementary sequence thereof.

The sequence of said first probe may e.g., consist of or comprise ahybridization portion, which is or acts as the hybridization portion ofthe probe, i.e., which is or acts as the DNA or RNA portion, whichconfers to the first probe the capacity to hybridize to the cDNAreverse-transcript of said first P. jirovecii mitochondrial gene.

Said hybridization portion may e.g., be a DNA or RNA sequence of 17-21nucleotides (more particularly of 19 nucleotides), which hybridizes tothe sequence of SEQ ID NO; 1 or the sequence complementary to SEQ ID NO:1, more particularly to the sequence of SEQ ID NO: 10 or the sequencecomplementary to SEQ ID NO: 10, without hybridizing to any of SEQ ID NO.3 and the sequence complementary to SEQ ID NO: 3, or to any of SEQ IDNO: 2 and the sequence complementary to SEQ ID NO: 2, more particularlywithout hybridizing to any of SEQ ID NO: 3, the sequence complementaryto SEQ ID NO: 3, SEQ ID NO: 2 and the sequence complementary to SEQ IDNO: 2.

Said hybridization portion of said first probe may also not hybridize tohuman DNA or RNA.

Said hybridization portion of said first probe may specificallyhybridize to the sequence of SEQ ID NO; 1 or to the complementarysequence thereof, more particularly to the sequence of SEQ ID NO: 10 orto the complementary sequence thereof. For example, the hybridizationportion of said first probe is the (19 nucleotide-long) sequence of SEQID NO: 13 or the complementary sequence thereof.

The sequence of said first probe may consist of said hybridizationportion.

Alternatively, the sequence of said first probe may comprise other DNAor RNA sequence(s) in addition to said hybridization portion, e.g.,other DNA or RNA sequence(s) linked to the 5′ and/or 3′ terminal end(s)of said hybridization portion. This (these) other DNA or RNA sequence(s)should not (significantly) reduce the hybridization specificity of saidhybridization portion. Said other DNA or RNA sequence(s) may e.g., bebeacon arm(s), more particularly a 5′ beacon arm and a 3′ beacon arm,which impart a hairpin-configuration to said first probe whenunhybridized (e.g., the 3′ beacon arm is complementary to the 5′ beaconarm). The total length of said first probe advantageously is of 25-29nucleotides, or of 24-28 nucleotides, or of 23-27 nucleotides, or of22-36 nucleotides.

Said first probe may comprise (e.g., be covalently linked to) at leastone fluorophore (e.g., 6-carboxyfluorescein, or tetrachlorofluorescein)and/or at least one quencher (e.g., a carboxytetramethylrhodaminefluorescent dye (e.g., TAMRA®), the Black Hole Quencher®-0, the BlackHole Quencher®-1, the Black Hole Quencher®-2, the Black HoleQuencher®-3, or the Minor Groove Binder® quencher).

Said first probe may e.g., be a Locked Nucleic Acid (LNA) probe.

Said first probe may e.g., be a DNA or RNA probe.

For example, said first probe may be a TAQMAN® probe, i.e., a probe,wherein a fluorophore is covalently attached to its 5′-end and aquencher is covalently attached to its at the 3′-end (e.g., TAMRA® orBHQ®-1). A TAQMAN® probe is degraded by the 5′-3′ exonuclease activityof the PCR polymerase, thereby releasing the fluorophore from it (andfrom the proximity of the quencher).

Alternatively, said first probe may be a beacon probe, i.e., a probewhich in addition to said hybridization portion, comprises a beacon armlinked to the 5′ terminal end and a beacon arm linked to the 3′ terminalend (which impart a hairpin-configuration to said first probe whenunhybridized), and which carries a fluorophore covalently linked to oneof said two beacon arms, and a quencher linked to the other of said twobeacon arms.

Alternatively, said first probe may be a SCORPION® probe (i.e., a probe,which is linked to a fluorophore at one of its ends and which is linkedat the other end to a primer via a PCR blocker).

The quantification may also be performed using at least two of saidfirst probes (i.e., two different first probes) each comprising at leastone fluorophore (e.g., as LIGHTCYCLER® hybridization probes).

The Tm of the probe may be 4-10° C. higher than the Tm of the primerpair.

The quantification of the RNA transcripts of said second P. jiroveciimitochondrial gene may e.g., be performed using (at least one) secondprobe, which hybridizes to the cDNA reverse-transcript of said second P.jirovecii mitochondrial gene.

When said second P. jirovecii mitochondrial gene is the mtLSU gene, saidsecond probe may hybridize to the P. jirovecii mtLSU gene, which is ofSEQ ID NO: 1 or to the sequence complementary to SEQ ID NO: 1, moreparticularly to the sequence of SEQ ID NO: 10 (a P. jirovecii mtLSUtarget) or to the sequence complementary to SEQ ID NO: 10.

More particularly, said second probe may hybridize to the sequence ofSEQ ID NO: 1 or the complementary sequence thereof, more particularly tothe sequence of SEQ ID NO: 10 or the complementary sequence thereof,without hybridizing to any of SEQ ID NO: 3 (P. jirovecii CYTB gene) andthe sequence complementary to SEQ ID NO: 3 or, to any of SEQ ID NO: 2(P. jirovecii mtSSU gene) and the sequence complementary to SEQ ID NO:2, more particularly without hybridizing to any of SEQ ID NO: 3, thesequence complementary to SEQ ID NO: 3, SEQ ID NO: 2 and the sequencecomplementary to SEQ ID NO: 2.

Said second probe may also not hybridize to human DNA or RNA.

Advantageously, said second probe specifically hybridizes to thesequence of SEQ ID NO: 1 or the complementary sequence thereof, moreparticularly to the sequence of SEQ ID NO: 10 or the complementarysequence thereof.

The sequence of said second probe may e.g., consist of or comprise ahybridization portion, which is or acts as the hybridization portion ofthe probe, i.e., which is or acts as the DNA or RNA portion, whichconfers to the second probe the capacity to hybridize to the cDNAreverse-transcript of said second P. jirovecii mitochondrial gene.

Said hybridization portion may e.g., be a DNA or RNA sequence of 17-21nucleotides (more particularly of 19 nucleotides), which hybridizes tothe sequence of SEQ ID NO; 1 or the sequence complementary to SEQ ID NO:1, more particularly to the sequence of SEQ ID NO: 10 or the sequencecomplementary to SEQ ID NO: 10, without hybridizing to any of SEQ ID NO;3 and the sequence complementary to SEQ ID NO: 3, or to any of SEQ IDNO: 2 and the sequence complementary to SEQ ID NO: 2, more particularlywithout hybridizing to any of SEQ ID NO: 3, the sequence complementaryto SEQ ID NO: 3, SEQ ID NO: 2 and the sequence complementary to SEQ IDNO: 2.

Said hybridization portion of said second probe may also not hybridizeto human DNA or RNA. Said hybridization portion of said second probe mayspecifically hybridize to the sequence of SEQ ID NO: 1 or to thecomplementary sequence thereof, more particularly to the sequence of SEQID NO: 10 or to the complementary sequence thereof. For example, thehybridization portion of said second probe is the (19 nucleotide-long)sequence of SEQ ID NO: 13 or the complementary sequence thereof.

The sequence of said second probe may consist of said hybridizationportion.

Alternatively, the sequence of said second probe may comprise other DNAor RNA sequence(s) in addition to said hybridization portion, e.g.,other DNA or RNA sequence(s) linked to the 5′ and/or 3′ terminal end(s)of said hybridization portion. This (these) other DNA or RNA sequence(s)should not (significantly) reduce the hybridization specificity of saidhybridization portion. Said other DNA or RNA sequence(s) may e.g., bebeacon arm(s), more particularly a 5′ beacon arm and a 3′ beacon arm,which impart a hairpin-configuration to said second probe whenunhybridized (e.g., the 3′ beacon arm is complementary to the 5′ beaconarm). The total length of said second probe advantageously is of 25-29nucleotides, or of 24-28 nucleotides, or of 23-27 nucleotides, or of22-36 nucleotides.

Said second probe may comprise (e.g., be covalently linked to) at leastone fluorophore (e.g., 6-carboxyfluorescein, or tetrachlorofluorescein)and/or at least one quencher (e.g., a carboxytetramethylrhodaminefluorescent dye (e.g., TAMRA®), the Black Hole Quencher®-0, the BlackHole Quencher®-1, the Black Hole Quencher®-2, the Black HoleQuencher®-3, or the Minor Groove Binder® quencher).

Said second probe may e.g., be a Locked Nucleic Acid (LNA) probe.

Said second probe may e.g., be a DNA or RNA probe.

For example, said second probe may be a TAQMAN® probe, i.e., a probe,wherein a fluorophore is covalently attached to its 5′-end and aquencher is covalently attached to its at the 3′-end (e.g., TAMRAX orBHQ-1). A TAQMAN@ probe is degraded by the 5′-3′ exonuclease activity ofthe PCR polymerase, thereby releasing the fluorophore from it (and fromthe proximity of the quencher).

Alternatively, said second probe may be a beacon probe, i.e., a probewhich in addition to said hybridization portion, comprises a beacon armlinked to the 5′ terminal end and a beacon arm linked to the 3′ terminalend (which impart a hairpin-configuration to said second probe whenunhybridized), and which carries a fluorophore covalently linked to oneof said two beacon arms, and a quencher linked to the other of said twobeacon arms.

Alternatively, said second probe may be a SCORPION® probe (i.e., aprobe, which is linked to a fluorophore at one of its ends and which islinked at the other end to a primer via a PCR blocker).

The quantification may also be performed using at least two of saidsecond probes (i.e., two different second probes) each comprising atleast one fluorophore (e.g., as LIGHTCYCLER® hybridization probes).

The Tm of the probe may be 4-10° C. higher than the Tm of the primerpair.

For example, when said second P. jirovecii mitochondrial gene is the P.jirovecii gene, the sequence of which codes for the Cytb protein, saidsecond probe may hybridize to the sequence of SEQ ID NO: 3 or thecomplementary sequence thereof, more particularly to the sequence of SEQID NO: 30 or the complementary sequence thereof, without hybridizing toany of SEQ ID NO: 1 (P. jirovecii mtLSU gene) and the sequencecomplementary to SEQ ID NO: 1, or to any of SEQ ID NO: 2 (P. jiroveciimtSSU gene) and the sequence complementary to SEQ ID NO: 2, moreparticularly to any of SEQ ID NO: 1, the sequence complementary to SEQID NO: 1, SEQ ID NO: 2 and the sequence complementary to SEQ ID NO: 2.Said second probe may also not hybridize to human DNA or RNA.Advantageously, said second probe specifically hybridizes to thesequence of SEQ ID NO: 3 or the complementary sequence thereof, moreparticularly to the sequence of SEQ ID NO: 30 or the complementarysequence thereof.

The sequence of said second probe may e.g., consist of or comprise ahybridization portion, which is or acts as the hybridization portion ofthe probe, i.e., which is or acts as the DNA or RNA portion, whichconfers to the second probe the capacity to hybridize to the cDNAreverse-transcript of said second P. jirovecii mitochondrial gene.

Said hybridization portion may e.g., be a DNA or RNA sequence of 19-30nucleotides (more particularly of 20-24 nucleotides, more particularlyof 22 nucleotides), which hybridizes to the sequence of SEQ ID NO: 3 orthe sequence complementary to SEQ ID NO: 3, more particularly to thesequence of SEQ ID NO: 30 or the sequence complementary to SEQ ID NO:30, without hybridizing to any of SEQ ID NO: 1 and the sequencecomplementary to SEQ ID NO: 1, or to any of SEQ ID NO: 2 and thesequence complementary to SEQ ID NO: 2, more particularly to any of SEQID NO: 1, the sequence complementary to SEQ ID NO: 1. SEQ ID NO: 2 andthe sequence complementary to SEQ ID NO: 2. Said hybridization portionof said second probe may also not hybridize to human DNA or RNA.

Said hybridization portion of said second probe may specificallyhybridize to the sequence of SEQ ID NO: 3 or to the complementarysequence thereof, more particularly to the sequence of SEQ ID NO: 30 orto the complementary sequence thereof. For example, the hybridizationportion of said second probe is the (22 nucleotide-long) sequence of SEQID NO: 33 or the complementary sequence thereof, or a LNA-counterpartthereof, such as the (22 nucleotide-long) sequence of SEQ ID NO: 58 orthe complementary sequence thereof (SEQ ID NO: 59; cf. example 3 below).

The sequence of said second probe may consist of said hybridizationportion.

Alternatively, the sequence of said second probe may comprise other DNAor RNA sequence(s) in addition to said hybridization portion, e.g.,other DNA or RNA sequence(s) linked to the 5′ and/or 3′ terminal end(s)of said hybridization portion. This (these) other DNA or RNA sequence(s)should not (significantly) reduce the hybridization specificity of saidhybridization portion. Said other DNA or RNA sequence(s) may e.g., bebeacon arm(s), more particularly a 5′ beacon arm and a 3′ beacon arm,which impart a hairpin-configuration to said second probe whenunhybridized (e.g., the 3′ beacon arm is complementary to the 5′ beaconarm). The total length of said second probe advantageously is of 28-32nucleotides, or of 27-31 nucleotides, or of 26-30 nucleotides, or of25-29 nucleotides.

Said second probe may comprise (e.g., be covalently linked to) at leastone fluorophore (e.g., 6-carboxyfluorescein, or tetrachlorofluorescein)and/or at least one quencher (e.g., a carboxytetramethylrhodaminefluorescent dye (e.g., TAMRA®), the Black Hole Quencher®-0, the BlackHole Quencher®-1, the Black Hole Quencher®-2, the Black HoleQuencher®-3, or the Minor Groove Binder® quencher).

Said second probe may e.g., be a Locked Nucleic Acid (LNA) probe.

Said second probe may e.g., be a DNA or RNA probe. For example, saidsecond probe may be a TAQMAN® probe, i.e., a probe, wherein afluorophore is covalently attached to its 5′-end and a quencher iscovalently attached to its at the 3′-end (e.g., TAMRA® or BHQ®-1). ATAQMAN® probe is degraded by the 5′-3′ exonuclease activity of the PCRpolymerase, thereby releasing the fluorophore from it (and from theproximity of the quencher).

Alternatively, said second probe may be a beacon probe, i.e., a probewhich in addition to said hybridization portion, comprises a beacon armlinked to the 5′ terminal end and a beacon arm linked to the 3′ terminalend (which impart a hairpin-configuration to said second probe whenunhybridized), and which carries a fluorophore covalently linked to oneof said two beacon arms, and a quencher linked to the other of said twobeacon arms.

Alternatively, said second probe may be a SCORPION® probe (i.e., aprobe, which is linked to a fluorophore at one of its ends and which islinked at the other end to a primer via a PCR blocker).

The quantification may also be performed using at least two of saidsecond probes (i.e., two different second probes) each comprising atleast one fluorophore (e.g., as LIGHTCYCLER® hybridization probes).

The Tm of the probe may be 4-10° C. higher than the Tm of the primerpair.

When said second P. jirovecii mitochondrial gene is the mtSSU gene, saidsecond probe may hybridize to

-   -   the P. jirovecii mtSSU gene, which is of SEQ ID NO: 2 or to the        sequence complementary to SEQ ID NO: 2, more particularly to the        sequence of SEQ ID NO: 15 (a P. jirovecii mtSSU target) or to        the sequence complementary to SEQ ID NO: 15, and/or    -   to the sequence of SEQ ID NO: 20 (another P. jirovecii mtSSU        target) or to the sequence complementary to SEQ ID NO: 20,        and/or    -   to the sequence of SEQ ID NO: 25 (still another P. jirovecii        mtSSU target) or to the sequence complementary to SEQ ID NO: 25.

More particularly, said second probe may hybridize to the sequence ofSEQ ID NO: 2 or the complementary sequence thereof, more particularly toat least one of the sequences of SEQ ID NO: 15, 20, 25 and thecomplementary sequences thereof, without hybridizing to any of SEQ IDNO: 3 (P. jirovecii CYTB gene) and the sequence complementary to SEQ IDNO: 3, or to any of SEQ ID NO: 1 and the sequence complementary to SEQID NO: 1, more particularly without hybridizing to any of SEQ ID NO: 3,the sequence complementary to SEQ ID NO: 3, SEQ ID NO: 1 and thesequence complementary to SEQ ID NO: 1.

Said second probe may also not hybridize to human DNA or RNA.

Advantageously, said second probe specifically hybridizes to thesequence of SEQ ID NO: 2 or the complementary sequence thereof, moreparticularly to at least one of the sequences of SEQ ID NO: 15, 20, 25and the complementary sequences thereof.

The sequence of said second probe may e.g., consist of or comprise ahybridization portion, which is or acts as the hybridization portion ofthe probe, i.e., which is or acts as the DNA portion, which confers tothe second probe the capacity to hybridize to the cDNAreverse-transcript of said second P. jirovecii mitochondrial gene.

Said hybridization portion may e.g., be a DNA sequence of 23-29nucleotides (more particularly of 25-27 nucleotides), which hybridizesto the sequence of SEQ ID NO: 2 or the sequence complementary to SEQ IDNO: 2, more particularly to at least one of the sequences of SEQ ID NO:15, 20, 25 and the sequences complementary to SEQ ID NO: 10, 20, 25,without hybridizing to any of SEQ ID NO: 3 and the sequencecomplementary to SEQ ID NO: 3, or to any of SEQ ID NO: 1 and thesequence complementary to SEQ ID NO: 1, more particularly withouthybridizing to any of SEQ ID NO: 3, the sequence complementary to SEQ IDNO: 3, SEQ ID NO: 1 and the sequence complementary to SEQ ID NO: 1.

Said hybridization portion of said second probe may also not hybridizeto human DNA or RNA. Said hybridization portion of said second probe mayspecifically hybridize to the sequence of SEQ ID NO: 2 or to thecomplementary sequence thereof, more particularly to at least one of thesequences of SEQ ID NO: 15, 20, 25 and the complementary sequencesthereof. For example, the hybridization portion of said second probe isthe (25 or 27 nucleotide-long) sequence of SEQ ID NO: 18, 23 or 28 orthe complementary sequence thereof.

The sequence of said second probe may consist of said hybridizationportion.

Alternatively, the sequence of said second probe may comprise other DNAsequence(s) in addition to said hybridization portion, e.g., other DNAsequence(s) linked to the 5′ and/or 3′ terminal end(s) of saidhybridization portion. This (these) other DNA sequence(s) should not(significantly) reduce the hybridization specificity of saidhybridization portion. Said other DNA sequence(s) may e.g., be beaconarm(s), more particularly a 5′ beacon arm and a 3′ beacon arm, whichimpart a hairpin-configuration to said second probe when unhybridized(e.g., the 3′ beacon arm is complementary to the 5′ beacon arm). Thetotal length of said second probe advantageously is of 31-37nucleotides, or of 30-36 nucleotides, or of 29-36 nucleotides, or of28-34 nucleotides.

Said second probe may comprise at least one fluorophore (e.g.,6-carboxyfluorescein, or tetrachlorofluorescein) and/or at least onequencher (e.g., a carboxytetramethylrhodamine fluorescent dye (e.g.,TAMRA®), the Black Hole Quencher®-0, the Black Hole Quencher®-1, theBlack Hole Quencher®-2, the Black Hole Quencher®-3, or the Minor GrooveBinder® quencher).

Said second probe may be a TAQMAN® probe, i.e., a probe, wherein afluorophore is covalently attached to its 5′-end and a quencher iscovalently attached to its at the 3′-end (e.g., TAMRA® or BHQ®-1). ATAQMAN® probe is degraded by the 5′-3′ exonuclease activity of the PCRpolymerase, thereby releasing the fluorophore from it (and from theproximity of the quencher).

Alternatively, said second probe may be a beacon probe, i.e., a probewhich in addition to said hybridization portion, comprises a beacon armlinked to the 5′ terminal end and a beacon arm linked to the 3′ terminalend (which impart a hairpin-configuration to said second probe whenunhybridized), and which carries a fluorophore covalently linked to oneof said two beacon arms, and a quencher linked to the other of said twobeacon arms.

The Tm of the probe may be 4-10° C. higher than the Tm of the primerpair.

Advantageously, said at least one first probe is implemented inreal-time PCR. More particularly, said at least one first probeadvantageously is implemented in the same tube as said first primer pairin real-time PCR amplification.

Advantageously, said at least one second probe in implemented inreal-time PCR. More particularly, said at least one second probeadvantageously is implemented in the same tube as said second primerpair in real-time PCR amplification.

Advantageously, said at least one first probe and one second probe areimplemented in real-time PCR. More particularly, said at least one firstprobe and said at least one second probe are implemented in the sametube as said first primer pair and second primer pair in real-time PCRamplification.

The application also relates to each individual product that isimplemented or obtainable by a method of the application.

More particularly, the application also relates to each of said firstprimer pair, said second primer pair, said first probe and said secondprobe, individually as a product.

More particularly, the application also relates to each of said firstcDNA targets, said second cDNA targets, said first RNA targets, saidsecond RNA targets, said first amplicons and said second amplicons,individually as a product.

The application also relates to the association or combinations of suchproducts.

More particularly, the application relates to the association orcombination of at least two or at least three different elements fromthe following list of four (different) elements: said first primer pair,said second primer pair, said first probe and said second probe; or tothe association or combination of the four of them.

More particularly, the application relates to the association orcombination of said first probe and said second probe.

More particularly, the application relates to the association orcombination of said first primer pair and said second primer pair.

More particularly, the application relates to the association orcombination of said first primer pair and said first probe.

More particularly, the application relates to the association orcombination of said second probe and said second primer pair.

For example, they can be associated or combined in a kit, moreparticularly in a kit for simultaneous, separate or sequential use, orin a composition, more particularly in a liquid composition, such as anamplification composition. Said association, combination, kit orcomposition may further comprise at least one reverse transcriptase(i.e., at least one RNA-dependent DNA polymerase), or at least onereverse transcriptase and at least one DNA-dependent DNA polymerase.

Advantageously, said kit comprises at least said first primer pairand/or at least said first probe, more particularly at least said primerpair and at least said first probe.

Said kit may further comprise an internal control for RNA extractionand/or purification, such as an IECR or such as at least one (real-time)probe, more particularly at least one (real-time) probe and at least oneprimer pair, which specifically detect a human gene (cf. above andexample 2 below).

More particularly, the application relates to the association orcombination of at least two or at least three or at least four or atleast five different elements from the following list of six (different)elements: said first cDNA targets, said second cDNA targets, said firstRNA targets, said second RNA targets, said first amplicons and saidsecond amplicons; or to the association or combination of the six ofthem. More particularly, the application relates to the association orcombination of said first amplicons and said second amplicons. Each ofsaid six elements can be contained in a composition, more particularlyin a liquid composition, such as an amplification composition. Saidassociation, combination or composition may further comprise at leastone reverse transcriptase (i.e., at least one RNA-dependent DNApolymerase), or at least one reverse transcriptase and at least onepolymerase (more particularly at least one DNA-dependent DNApolymerase).

Said reverse transcriptase (or said reverse transcriptase andDNA-dependent DNA polymerase) can be any reverse transcriptase (or anyreverse transcriptase and DNA-dependent DNA polymerase), which theperson of average skill in the art may find appropriate.

Examples of reverse transcriptase include the SUPERSCRIPT® III ReverseTranscriptase (RT) commercialized by INVITROGEN™ (INVITROGEN™ by LIFETECHNOLOGIES™; 5791 Van Allen way: Carlsbad; Calif. 92008, U.S.A.).

Examples of polymerases (i.e., of DNA-dependent DNA polymerases) includea Thermus aquaticus polymerase.

Said product(s), association(s), combination(s), kit(s), composition(s)is(are) suitable for diagnosing or predicting PneumoCystis Pneumonia(PCP), more particularly for diagnosing or predicting whether a humanpatient (more particularly a human patient, who is a Pneumocystisjirovecii carrier) has or develops PCP, or for determining or predictingthe efficacy of a drug or treatment against PCP in a human patient (moreparticularly a human patient, who is a Pneumocystis jirovecii carrier),or for determining whether PCP regresses or has been treated in a humanpatient who has been diagnosed to have PCP and who is receiving or hasreceived a drug or treatment against PCP.

The application thus also relates to the (in vitro) use of saidproduct(s), association(s), combination(s), kit(s), composition(s) fordiagnosing or predicting PneumoCystis Pneumonia (PCP), more particularlyfor diagnosing or predicting whether a human patient (more particularlya human patient, who is a Pneumocystis jirovecii carrier) has ordevelops PCP, or for determining or predicting the efficacy of a drug ortreatment against PCP in a human patient (more particularly a humanpatient, who is a Pneumocystis jirovecii carrier), or for determiningwhether PCP regresses or has been treated in a human patient who hasbeen diagnosed to have PCP and who is receiving or has received a drugor treatment against PCP.

More particularly, the application relates to the in vitro use of areverse transcriptase (i.e., a RNA-dependent DNA polymerase) and ofoligonucleotides:

-   -   for diagnosing or predicting PneumoCystis Pneumonia (PCP), more        particularly for diagnosing or predicting whether a human        patient (more particularly a human patient, who is a        Pneumocystis jirovecii carrier) has or develops PCP, or    -   for determining or predicting the efficacy of a drug or        treatment against PCP in a human patient (more particularly a        human patient, who is a Pneumocystis jirovecii carrier), or    -   for determining whether PCP regresses or has been treated in a        human patient who has been diagnosed to have PCP and who is        receiving or has received a drug or treatment against PCP,        wherein said oligonucleotides comprise primers and/or probes,        wherein said primers comprises a first primer pair and a second        primer pair, wherein said probes comprise a first probe and a        second probe,        wherein said first primer pair and/or said first probe        specifically hybridizes to the cDNA reverse transcripts of the        RNA transcripts of said first P. jirovecii mitochondrial gene        (cf. above),        wherein said second primer pair and/or said second probe        specifically hybridizes to the cDNA reverse transcripts of the        RNA transcripts of said second P. jirovecii mitochondrial gene        (cf. above).

For example, said first P. jirovecii mitochondrial gene is the P.jirovecii gene, the sequence of which codes for the Cytb protein, andsaid second P. jirovecii mitochondrial gene is a P. jirovecii gene, thesequence of which transcribes into a P. jirovecii ribosomal RNA (mtLSUgene or mtSSU gene, more particularly mtLSU gene).

For example, said first P. jirovecii mitochondrial gene is the mtSSU P.jirovecii gene, and said second P. jirovecii mitochondrial gene is theP. jirovecii mtLSU gene.

Said use may further comprises the use of a polymerase (i.e., of aDNA-dependent DNA polymerase).

Said use may further comprise the use a RNA extraction and/orpurification internal control, such as an IECR or such as at least one(real-time) probe, more particularly at least one (real-time) probe andat least one primer pair, which specifically detect a human gene (cf.above and example 2 below).

The application also relates to a kit, which comprises said reversetranscriptase and said oligonucleotides. Said kit may further comprise apolymerase (i.e., a DNA-dependent DNA polymerase). Said kit can beviewed as a kit suitable for diagnosing or predicting PneumoCystisPneumonia (PCP) in a human patient (more particularly, a human patient,who is a Pneumocystis jirovecil carrier), or for determining orpredicting the efficacy of a drug or treatment against PCP in a humanpatient (more particularly, a human patient, who is a Pneumocystisjirovecil carrier), or for determining whether PCP regresses or has beentreated in a human patient who has been diagnosed to have PCP and whoreceives or has received a drug or treatment against PCP. Said kit mayfurther comprise written instructions for implementing said reversetranscriptase and said oligonucleotides (and optionally said polymerase)in these uses or applications.

Said kit may be a kit for simultaneous, separate or sequential use, moreparticularly for simultaneous use, of said reverse transcriptase andsaid oligonucleotides (or of said reverse transcriptase, saidoligonucleotides and said polymerase). Said kit may comprisecontainer(s) (e.g., tube(s)), wherein said reverse transcriptase andsaid oligonucleotides (or said reverse transcriptase, saidoligonucleotides and said polymerase) are contained. Advantageously,said reverse transcriptase and said polymerase are contained in the samecontainer (e.g., in the same tube). Said first primer pair can becontained in a container (e.g., tube), which is different from thecontainer (e.g., tube) in which said second primer pair is contained.Said first probe can be contained in a container (e.g., tube), which isdifferent from the container (e.g., tube) in which said second probe iscontained. Said first primer pair and said first probe may be in thesame container (e.g., tube). Said second primer pair and said secondprobe may be in the same container (e.g., tube).

Said kit may further comprise means for RNA extraction and/orpurification. For example, said kit may further comprise cell lysisreagent(s) and/or buffer(s), and/or RNA purification means, such ase.g., a silica membrane.

Said kit may further comprise an internal control for RNA extractionand/or purification such as an IECR or such as at least one (real-time)probe, more particularly at least one (real-time) probe and at least oneprimer pair, which specifically detect a human gene (cf. above andexample 2 below).

Each feature or combination of features, which has been described in thecontext of a method of the application, applies to each product,combination, association, kit or composition as such as well as to theiruses, mutatis mutandis.

For example, the nucleotide sequence of each primer of said first andsecond primer pairs may independently consist of 15-30 nucleotides(e.g., of 18-28 or 19-27 or 20-26 nucleotides) (cf. above).

For example, the nucleotide sequence of each of said first and secondprobes independently consists of 17-37 nucleotides (e.g., of 20-24 or28-32 or 17-21 or 25-29 or 23-29 or 31-37 nucleotides) (cf. above).

For example, said first or second primer pair is a primer pair, whichanneals to the cDNA reverse transcripts of the RNA transcripts of saidfirst or second P. jirovecii mitochondrial gene (or to the RNAtranscripts of said first or second P. jirovecii mitochondrial gene aswell as to the cDNA reverse transcripts thereof) to produce a cDNAamplicon, which is of 100-120 nucleotide-long (more particularly of100-110 nucleotide-long, more particularly of 102-108 nucleotide-long,more particularly of 104-106 nucleotide-long, more particularly of 105nucleotide-long), and which comprises or is

-   -   the sequence of SEQ ID NO: 30, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 30        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID        NO: 30. For example, said first or second primer pair is the        primer pair of SEQ ID NO: 31 and SEQ ID NO: 32. For example,        said first or second primer pair is the primer pair of SEQ ID        NO: 60 and SEQ ID NO: 32.

For example, said first or second primer pair may e.g., be a (mtLSU)primer pair, which anneals to the cDNA reverse transcripts of the RNAtranscripts of the P. jirovecii mtLSU gene (or to the RNA transcripts ofthe P. jirovecii mtLSU gene as well as to the cDNA reverse transcriptsthereof) to produce a cDNA amplicon, which is of 115-125 nucleotides(more particularly of 117-124 nucleotides, more particularly of 119-123nucleotides, more particularly of 121 nucleotides), and which comprisesor is

-   -   the sequence of SEQ ID NO: 10, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 10        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID        NO: 10. For example, said first or second primer pair is the        (mtLSU) primer pair of SEQ ID NO: 11 and SEQ ID NO: 12.

For example, said first or second primer pair may alternatively be a(mtSSU) primer pair, which anneals to the cDNA reverse transcripts ofthe RNA transcripts of the P. jirovecii mtSSU gene (or to the RNAtranscripts of the P. jirovecii mtSSU gene as well as to the cDNAreverse transcripts thereof) to produce a cDNA amplicon, which is of60-110 nucleotides (more particularly of 76-92 nucleotides, moreparticularly of 76, 82 or 92 nucleotides, more particularly of 82nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 15, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 15        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID        NO: 15. For example, said first or second primer pair is the        (mtSSU) primer pair of SEQ ID NO: 16 and SEQ ID NO: 17.

For example, said first or second primer pair may alternatively be a(mtSSU) primer pair, which anneals to the cDNA reverse transcripts ofthe RNA transcripts of the P. jirovecii mtSSU gene (or to the RNAtranscripts of the P. jirovecil mtSSU gene as well as to the cDNAreverse transcripts thereof) to produce a cDNA amplicon, which is of60-110 nucleotides (more particularly of 76-92 nucleotides, moreparticularly of 76, 82 or 92 nucleotides, more particularly of 92nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 20, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 20        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID        NO: 20. For example, said first or second primer pair is the        (mtSSU) primer pair of SEQ ID NO: 21 and SEQ ID NO: 22.

For example, said first or second primer pair may alternatively be a(mtSSU) primer pair, which anneals to the cDNA reverse transcripts ofthe RNA transcripts of the P. jirovecii mtSSU gene (or to the RNAtranscripts of the P. jirovecii mtSSU gene as well as to the cDNAreverse transcripts thereof) to produce a cDNA amplicon, which is of60-110 nucleotides (more particularly of 76-92 nucleotides, moreparticularly of 76, 82 or 92 nucleotides, more particularly of 76nucleotides), and comprises or is

-   -   the sequence of SEQ ID NO: 25, or    -   a cDNA sequence, which is of the same length as SEQ ID NO: 25        and which is at least 95% (more particularly at least 96%, at        least 97%, at least 98% or at least 99%) identical to SEQ ID        NO: 25. For example, said first or second primer pair is the        (mtSSU) primer pair of SEQ ID NO: 26 and SEQ ID NO: 27.

In accordance with the understanding of the person of average skill inthe art, a primer pair, which anneals to a (target) cDNA or RNA or DNA,can be viewed as a pair of forward and reverse primers. The forwardprimer anneal to a first sequence, which is contained in said (target)cDNA or RNA or DNA, and the reverse primer anneals to a second sequence,which is contained in the sequence complementary to said (target) cDNAor RNA or DNA. The 5′ end of said first (target) sequence and the 5′ endof said second (target) sequence can be viewed as the start and endpositions of the amplicon produced by said primer pair.

More particularly, and still in accordance with the understanding of theperson of average skill in the art, a primer pair, which anneals to a(target) cDNA or RNA or DNA, can be viewed as a primer pair, wherein:

-   -   a first primer of the pair is at least 95% (more particularly at        least 96%, at least 97%, at least 98% or at least 99%) identical        to a first sequence, which is contained in said (target) cDNA or        RNA or DNA, and which is of the same length as said first        primer, and    -   the second primer of the same pair is at least 95% (more        particularly at least 96%, at least 97%, at least 98% or at        least 99%) identical to a second sequence, which is contained in        the sequence complementary to said (target) cDNA or RNA or DNA        and which is of the same length as said second primer.

In accordance with the understanding of the person of average skill inthe art, the 5′ end of said first (target) sequence and the 5′ end ofsaid second (target) sequence can be viewed as the start and endpositions of the amplicon produced by said primer pair.

The application also relates to a solid support, such as a nucleic acidmicroarray, nanoarray, chip or lane, onto which said first primer pairand/or said first probe is/are attached or bound. Said solid support mayfurther comprise said second primer pair and/or said second probeattached or bound thereto. Said solid support may e.g., be a plastic,glass or silicon microarray, nanoarray, chip or lane.

The application also relates to the (in vitro) use of a P. jiroveciltranscriptome for diagnosing or predicting PneumoCystis Pneumonia (PCP),more particularly for diagnosing or predicting whether a human patient(more particularly a human patient, who is a Pneumocystis jiroveciicarrier) has or develops PCP, or for determining or predicting theefficacy of a drug or treatment against PCP in a human patient (moreparticularly a human patient, who is a Pneumocystis jirovecii carrier),or for determining whether PCP regresses or has been treated in a humanpatient who has been diagnosed to have PCP and who is receiving or hasreceived a drug or treatment against PCP. Said use comprises detectingand/or quantifying, more particularly quantifying. (the number of or theconcentration of) the RNA transcripts of said first P. jiroveciimitochondrial gene and (the number of or the concentration of) the RNAtranscripts of said second P. jirovecii mitochondrial gene. For example,said use comprises detecting and/or quantifying, more particularlyquantifying, (the number of or the concentration of) the RNA transcriptsof said first P. jirovecii mitochondrial gene (CYTB gene) and (thenumber of or the concentration of) the RNA transcripts of said second P.jirovecii mitochondrial gene (mtLSU or mtSSU, more particularly mtLSU).For example, said use comprises detecting and/or quantifying, moreparticularly quantifying, (the number of or the concentration of) theRNA transcripts of said first P. jirovecii mitochondrial gene (mtSSU)and (the number of or the concentration of) the RNA transcripts of saidsecond P. jirovecii mitochondrial gene (mtLSU).

The application also relates to a nucleic acid library, which is orcomprises the transcriptome of P. jirovecii, more particularly the RNAtranscripts of P. jirovecii. This transcriptome or transcripts can bethose of a patient's biological sample as discussed above. Such alibrary is useful for detecting and/or quantifying, more particularlyquantifying, (the number of or the concentration of) the RNA transcriptsof said first P. jirovecii mitochondrial gene and (the number of or theconcentration of) the RNA transcripts of said second P. jiroveciimitochondrial gene. For example, such a library is useful for detectingand/or quantifying, more particularly quantifying, (the number of or theconcentration of) the RNA transcripts of said first P. jiroveciimitochondrial gene (CYTB gene) and (the number of or the concentrationof) the RNA transcripts of said second P. jirovecii mitochondrial gene(mtLSU or mtSSU). For example, such a library is useful for detectingand/or quantifying, more particularly quantifying, (the number of or theconcentration of) the RNA transcripts of said first P. jiroveciimitochondrial gene (mtSSU) and (the number of or the concentration of)the RNA transcripts of said second P. jirovecii mitochondrial gene(mtLSU).

The library of the application is notably suitable for high throughputsequencing, e.g., for implementation of the RNA-Seq method described inWang et al. 2009.

Said library can be used in accordance with the application, e.g., fordiagnosing or predicting PneumoCystis Pneumonia (PCP), more particularlyfor diagnosing or predicting whether a human patient (more particularlya human patient, who is a Pneumocystis jirovecii carrier) has ordevelops PCP, or for determining or predicting the efficacy of a drug ortreatment against PCP in a human patient (more particularly a humanpatient, who is a Pneumocystis jirovecii carrier), or for determiningwhether PCP regresses or has been treated in a human patient who hasbeen diagnosed to have PCP and who is receiving or has received a drugor treatment against PCP.

Said nucleic acid library can e.g., be a DNA library, which comprises orconsists of DNA fragments of 40-400 bp, wherein each of said DNAfragments comprise the cDNA reverse transcript of a P. jirovecii RNAfragment of 40-400 nucleotides, wherein said P. jirovecii RNA fragmentof 40-400 nucleotides is a fragment of 40-400 nucleotides from the RNAtranscript of a P. jirovecii mitochondrial gene.

Advantageously, said P. jirovecii mitochondrial gene is the mtLSU gene,the mtSSU or the CYTB gene.

Advantageously, said DNA library comprises or consists of:

-   -   at least one first DNA fragment of 40-400 bp, which comprises        the cDNA reverse transcript of a fragment of 40-400 nucleotides        from the RNA transcript of the P. jirovecii, CYTB gene and    -   at least one second DNA fragment of 40-400 bp, which comprises        the cDNA reverse transcript of a fragment of 40-400 nucleotides        from the RNA transcript of the P. jirovecil mtLSU or mtSSU gene,        wherein said fragment of 40-400 nucleotides from the RNA        transcript of the P. jirovecii CYTB gene is different from said        fragment of 40-400 nucleotides from the RNA transcript of the P.        jirovecii mtLSU or mtSSU gene.

Advantageously:

-   -   said fragment of 40-400 nucleotides from the RNA transcript of        the P. jirovecii CYTB gene is specific of the RNA transcript of        the P. jirovecii CYTB gene,    -   said fragment of 40-400 nucleotides from the RNA transcript of        the P. jirovecii mtLSU gene is specific of the RNA transcript of        the P. jirovecii mtLSU gene,    -   said fragment of 40-400 nucleotides from the RNA transcript of        the P. jirovecii mtSSU gene is specific of the RNA transcript of        the P. jirovecii mtSSU gene.

Advantageously, said DNA library comprises or consists of:

-   -   at least one first DNA fragment of 40-400 bp, which comprises        the cDNA reverse transcript of a fragment of 40-400 nucleotides        from the RNA transcript of the P. jirovecii, mtSSU and    -   at least one second DNA fragment of 40-400 bp, which comprises        the cDNA reverse transcript of a fragment of 40-400 nucleotides        from the RNA transcript of the P. jirovecii mtLSU gene,        wherein said fragment of 40-400 nucleotides from the RNA        transcript of the P. jirovecii mtSSU gene is different from said        fragment of 40-400 nucleotides from the RNA transcript of the P.        jirovecii mtLSU.

In said DNA libraries, each of said DNA fragments may optionally furthercomprise:

-   -   a first DNA of 30-150 bp, which is not a fragment of P.        jirovecii cDNA or DNA, and which is (covalently) linked to the        5′ end said cDNA reverse transcript (e.g., a DNA of 30-150 bp,        which is a first sequencing adaptor), and    -   a second DNA of 30-150 bp, which is not a fragment of P.        jirovecii cDNA or DNA, and which is (covalently) linked to the        3′ end of said cDNA reverse transcript (e.g., a DNA of 30-150        bp, which is a second sequencing adaptor, different from said        first sequencing adapter).

The application also relates to a computer program product, for storagein a memory of a processing unit or on a removable memory support forcooperation with a reader of said processing unit, which comprises(code) instructions for carrying out a method of the application (whenread or executed by a processor or microprocessor).

More particularly, the computer program product of the application maycomprise (code) instructions, which (when read or executed by aprocessor or microprocessor) align RNA or cDNA sequence reads on themitochondrial DNA sequence of P. jirovecii to detect and/or quantify(the number of or the concentration of) the RNA transcripts of saidfirst P. jirovecii mitochondrial gene (e.g., cytb or mtSSU) and of saidsecond P. jirovecii mitochondrial gene (e.g., mtLSU or mtSSU).

The application also relates to a computer device, comprising aprocessing unit in the memory of which is stored the computer programproduct of the application, and measurement values for the respectivevalues of quantification of the RNA transcripts of said first P.jirovecii mitochondrial gene (e.g., cytb or mtSSU) and of said second P.jirovecii mitochondrial gene (e.g., mtLSU or mtSSU).

The application also relates to a kit for use in the treatment and/orprevention and/or palliation of PCP in a human patient, (moreparticularly, a human patient, who is a Pneumocystis jirovecii carrier),wherein comprises one or several ingredient(s) for simultaneous,separate or sequential use in said treatment and/or prevention and/orpalliation. Said one or several active ingredient(s) may e.g., be

-   -   (the combination or association of) at least one dihydrofolate        reductase inhibitor and at least one sulfonamide antibiotic,        e.g., (the combination or association of) trimethoprim and        sulfamethoxazole (e.g., the cotrimoxazole combination drug), or    -   aerosolized pentamidine, or    -   primaquine and clindamycin, or    -   atovaquone, or    -   pyrimethamine, or    -   echinocandin(s) (including caspofungin), or    -   corticosteroid(s) (including prednisone), or    -   anti-inflammatory active ingredient(s), or    -   dapsone, or    -   dapsone and pyrimethamine and leucovorin.

More particularly, said human patient is a human patient, who has beendiagnosed or predicted to be at high risk of having or developing PCPwith a method of the application.

The application also relates to a method for the treatment and/orprevention and/or palliation of PCP in a human patient in need thereof,wherein said human patient is a Pneumocystis jirovecii carrier. Saidmethod comprises:

-   -   diagnosing or predicting whether said human patient is at high        risk of having or developing PCP with a method of the        application,    -   providing a drug or a combination of drugs for the treatment        and/or prevention and/or palliation of PCP, and    -   administering said drug or a combination of drugs to said human        patient.

Said drug or combination of drugs may comprise

-   -   (the combination or association of) at least one dihydrofolate        reductase inhibitor and at least one sulfonamide antibiotic,        e.g., (the combination or association of) trimethoprim and        sulfamethoxazole (e.g., the cotrimoxazole combination drug), or    -   aerosolized pentamidine, or    -   primaquine and clindamycin, or    -   atovaquone, or    -   pyrimethamine, or    -   echinocandin(s) (including caspofungin), or    -   corticosteroid(s) (including prednisone), or    -   anti-inflammatory active ingredient(s), or    -   dapsone, or    -   dapsone and pyrimethamine and leucovorin.

The term “comprising”, which is synonymous with “including” or“containing”, is open-ended, and does not exclude additional, un-recitedelement(s), ingredient(s) or method step(s), whereas the term“consisting of” is a closed term, which excludes any additional element,step, or ingredient which is not explicitly recited.

The term “essentially consisting of” is a partially open term, whichdoes not exclude additional, un-recited element(s), step(s), oringredient(s), as long as these additional element(s), step(s) oringredient(s) do not materially affect the basic and novel properties ofthe invention.

The term “comprising” (or “comprise(s)”) hence includes the term“consisting of” (“consist(s) of”), as well as the term “essentiallyconsisting of” (“essentially consist(s) of”).

Accordingly, the term “comprising” (or “comprise(s)”) is, in theapplication, meant as more particularly encompassing the term“consisting of” (“consist(s) of”), and the term “essentially consistingof” (“essentially consist(s) of”).

In an attempt to help the reader of the present application, thedescription has been separated in various paragraphs or sections. Theseseparations should not be considered as disconnecting the substance of aparagraph or section from the substance of another paragraph or section.To the contrary, the application encompasses all the combinations of thevarious sections, paragraphs and sentences that can be contemplated.

Each of the relevant disclosures of all references cited herein isspecifically incorporated by reference. The following examples areoffered by way of illustration, and not by way of limitation.

EXAMPLES Example 1

Material and Methods

Samples

A total of 200 consecutive BronchoAlveolar Lavage (BAL) Fluids (BALF)were collected prospectively between the 1 Jan. 2013 and the 31 Aug.2013. Fiber optic bronchoscopy was performed after patients stated theirnon-opposition to the use of BALF for testing new diagnostic procedures.The site of BAL was guided by the topography of the lesions upon lunghigh-resolution computed tomography, and BAL was performed with four50-mL aliquots of sterile saline solution following the standardizedprotocol of Alanio et al. 2011. BALF was sent within the hour aftercollection to the laboratory. Upon arrival, the BALF was centrifuged at2,800 g for 10 minutes, the pellet was re-suspended with 4 mL ofphosphate-buffered saline and split in four fractions of 1 mL. The fourtubes were then centrifuged at 8,000 g for 5 minutes and the pellets oftwo tubes were frozen and stored at −80° C. The two other pellets wereused for classical staining, immunofluorescence procedure and DNAextraction as described in Alanio et al. 2011.

Classical staining, immunofluorescence and the Cq value of the DNA PCR(Alanio et al. 2011) were recorded for each BALF and also for anynon-invasive diagnostic specimen (mostly sputa and induced sputa)performed before the BALF.

Seven samples were repeated and were considered as new infectiousepisodes except if PCP diagnosis based on immunofluorescence waspositive before.

Patients

The 192 corresponding patients were cared for in three hospitals in thenorth of Paris (Hospital Saint Louis, 1 avenue Claude Vellefaux 75010Paris France; Hospital Lariboisière, 2 rue Ambroise Parè 75010 ParisFrance; and Hospital Robert Debrè, 48 Boulevard Serrurier 75019 ParisFrance). The sex ratio was 1.5 and the median age was 50 years with arange of 02 to 82 years. In the patients with evidence of P. jirovecil(immunofluorescence, DNA or RNA detection), the whole medical fileincluding clinical, radiological and biological features wasretrospectively analyzed by two expert physicians (one pneumologist andone infectious disease specialist). For specific analyses, the date ofintroduction and duration of cotrimoxazole therapy at the time of theBAL was recorded. Outcome at the last follow-up visit was recorded fromthe electronic medical file. Underlying diseases were divided into fourcategories (HIV positivity, hematological malignancies, solid organtransplantation, others).

Probability of PCP Classification

PneumoCystis pneumonia (PCP) diagnosis as the etiology of an acutepneumonia episode were classified as proven, probable, possible and noPCP. Criteria used for proven, probable, possible classification aresummarized in Table 1 below. Other clinical situations were classifiedas no PCP.

TABLE 1 Criteria used to classify patients regarding Pneumocystispneumonia (PCP) probability in a context of acute pneumonia episodeCompatible Compatible clinical and Favorable No Background radiologicaloutcome under No alternative Positive IF PCP (ID) presentation therapyprophylaxis diagnosis (BAL or IS)* Proven X X X X X Probable X X X X XPossible X X X X *based on BALF and sputa specimens.

RNA Extraction

The day of the experiment, the pellet of one tube was thawed and RNA wasextracted using the RNeasy® plus mini kit (catalog number 74136) fromQIAGEN® France S.A.S. (3 avenue du Canada: LP 809; 91974 COURTABOEUFCEDEX; FRANCE). Briefly: 350 μL of lysing buffer RLT+1%betamercaptoethanol were added to the pellet and vortexed. 350 μL ofethanol 70% were added and mixed gently. The final volume was depositedin the column and additional steps were performed following themanufacturer's recommendations. We obtained at the end 50 μL of RNAextracted.

Gene sequences The reference sequence used to design primersand a probe for the quantification of theRNA transcripts of the mitochondrial LargeSubUnit (mtLSU, also known as RNL) isreferenced in GENBANK® under the accession number JX499143.1 REGION:12373 . . . 15076 (SEQ ID NO: 1), which is: (SEQ ID NO: 1)AAAGGGGTTATTAAGGATAACTAGCTAATATATTTAAGGAGGTGTCGAATCCAAAATCATTATTCTAAAGATGTAATAATGTAAATCCGAGAGGGAAACCTCAATACTAATTACGAAGTGAAATGAAACATCTTAGTAACTTTAGGAAAAGAAATCAACCGAGATTTTATGAGTAGTGGTGAGCGAAAGTAAATTAGCCAAGTATTTATATAATAGATTAAATATAATTAATTACAAAAATTAATTGTAGTCTTCGAATGAAAGATCAATCTCCTCTTTTAAAAGTTGGAATGCTTTAGCCAAGGATGGTGAAAGCCCAGAGTCCCAGGAATATAAATACAAAATAAGTAGAACGAGAGATAACTTGTTTGAATACAGATAATATTTATGTAGTAATGTATGGAAGAATTCAACTTTATACTAATTACACATAAGATTATTAGGGGAACTATCCTCTAAGGCTAAATATAATATATTAAGCGATAGTGAAGAGTACCGTGAGGGAAAGTTGAAAAGAATATAAGTGAAACAGATCTTGAATTAATAACCTTATAAGCAGTCGGAGGTCCAAAGACTGACGACGTACCTTTTGGATAATGGGTCAGCAAGTTAATATGCAATGCAAGTCGCAAGACCTAATGAAGATGATTCTGAACAGGGATATAAAGTATTGTGTATTAGACCCGAAATCTAGTGATCTTACTATGATCAGACAACTTCAGGTCGAACTGGTGTACGTCGCAAAGTACTCAGAAGAATTGTGGTAAGTAGTGAAATACAAATCGGACTAGGATATAGCTGGTTTTCTGCGAAAATTGTTTTGGCAAATTGTTTATTCCTCTAAAAAATAGTAGGTATAGCACTGAATATCTCGAGGGAGTATGAAAATATTTATCTCAGATATTTAATCTCAAAATAACTATTTCTTAAAATAAATAATCAGACTATGTGCGATAAGGTAGATAGTCGAAAGGGAAACAGCCCAGAACAGTAATTAAAGCTCCCCAATTAATATTAAGTGAAATAAAAGTTGTTGGATATCTAAAACAGTTAAGAAGTGGGCTTGGAAAGAGCCATCTTTTAAAGAACACGTAAAAGTGCAATGATCTATGATCTCCAGCGCTGAAAATATCCGGATCTAAATATTATGCTGAAAGACTGTTTATTTTTCTTTTAATTAACTGTAATTTAATTAAAAAAAATAAGGTAGCAGAACATTTAGTAAATGTGTGAAGAATAGTATTTTATTATTCGGACATAACTAAAGAGAGAATGCTGACATGAGTAACGTTAAAATAGGTGAAAATCCTATTCGCCGAAAATGGAAGGTTTTTATAGTTCCGCTTAACTACTATAAATCAGATCGGTCTCTAACAGTAATTCGAATGAATAATGGATGAGAAACATATATAAAAATCGTAAGATTCAGGAAAAATTATATGTAATAACCGTACTAAAACCGACACAGGTCCATGAATATTAATGTATAGAGGCGAATGAGAGAATTATTGCGAAGGAACTCGGCAAATGAATTTCGTAATTTCGAGATAAGAAATACCAATGGTGTCAATAATGAGGTTGTACAACTGTTTACTTAAAACACAGTACTTTGCAAAGATTAAAAATCATTGTATAAAGTATGAAATCTGCCCAATGCTAAATGATAAAATCTATGGCTTCAATGGCTGTGGGTATAATGTTTAGTGAATGGCGGCCTTAACTATAAGGGTCCTAAGGTAGCGAATTTCCTTGGCCGTTAAATGCGGTCCCGCACGAATGATTTAATGATACAACAACTGTCTCCGGAATAAACTCAGTGAAATTGGATTAGCCGTGAAGATACGGTTTGTATATAGATAGACGGGAAGACCCTATGCAGCTTAACTGTTGTTCTTTATTGTTTTTTTAAATTCTCTTCTGTAGTGCTAAAAGGTAGTCGATGAGATGTCAGTGAAAAACCTTTGTGGAAATTTAAAATAACTAACTTACTTAATTAAGAACAGTGAAGATTAGACAGTTTCTGTGGGGCGCAGATCTCAAAAATTGTATCTGAGATGCCCAAAGGCATGGTGAAATTGGATGGTAACCAATGAATGTACATTTGTATATCTAGTGGTCTTTAATTACTAGATGATGTTTTATTTAATAAAGTGTAATGGCATAACTCATGCTTAACAGTAAGACTAAGAAGTCAAACTGACATGTAAGTGGGGCATAATGACCCTCGTTTACATTATGGATTGGAACGAGAGTAACGAATAAAAGCTACGCTAGGGATAACAGGGTTATTTCGTGTGAGAGATCGTATTGACCACGAAGTTTGCCACCTCGATGTCGACTCAACCTATCCTCCAGGAGTAGAATATTGGAAGGGTTCGGCTGTTGGCCGATTAAAAGGTTACGTGAGTTGGGTTAAAAACGTTGTGAAACAGTTTGGTTCCTATCTTCTATATATTTTAAAAGTTAATGGAGAATTTACTCTTTGTACGCAAGGATCAGATGTATTTTAACCTCTGGTTTGTCTGTTGTTTGTCGCATCGCAGATACGCTATGTTGATACGGAATAAATATTGAAAGCATATTAAATATGAAGTCCTACTCCATAAACTTTCTTGCGTTGTAGACTACGACGTAGATAGGCTTTATCTGTAAGAATAGTAATGTTTTAAGGTATAAAGTACTAATTTTTTTTTGACTGAATTAT.The reference sequence used to design primersand a probe for the quantification of theRNA transcripts of the mitochondrial SmallSubUnit (mtSSU, also known as RNS), isreferenced in GENBANK® under the accession number JX499143.1, REGION:31755 . . . 33192 (SEQ ID NO: 2), which is: (SEQ ID NO: 2)TAAGATAATTCACAAAAGAAAGAGTTTAATGTTAGCTCCGAATCAACGCTATCTAGAGGCATTACACATGCAAATCGTACGTTTAAAGTGGTGAACAGGTGAGTAAAGATAGAAATCTACCTATTCATAAGGTTAGATACCTTTTAAAAGAACAATTGTTTGTGAATAGATGAGTCTAAGTGGGGGAGGTAGTTGTGAGGTGAAGATCCTCCCAAGCCTAAGAACCCTAGTTATATTTGAAAGAATGAATAACCACATTGGCTCTGAAACAACAGCCAAGATTTTCATCCAAGAAAGTCCAGCAGTGGGGAATATTGGTCAATGATCGAAAGATTGAACCAGCTATCTAGAAGAATTTGTATTCTGTTATTAGAGAGGATTATGACGTTATCTAATTAAAGTCTCGACCAATTCTCGTGCCAGCAGTCGCGGTAAGACGAGTGAGGCTAGCGTTATTCATAATTATTAGGTCTAAAGGGTACGTAGATGGTTAACTTATCTGTTATTTATGTGTGAAGGAATTAGTATTCTAATTCGTTTTATTAGTATTCTAATTTTTTTAATAGAACATAAAAGAATTGGATAAATTGATTAACTAGAGTCGAATAGAAGAATAAAGAATTTTAAGAGTAGAGATGAAATTCAACGATACTTAAAGGACTGCCAATGGCGAAAGCATTATTCTAGGTAACGACTGACATTGAGGTACGTAGGCATAAGTAGCGAAAAGGATTAGATACCCTTGTAGTTTATGCTGTAAACGATGAATGCTAGAGGTCAGAATTTATTTATTTTTGGTCTTTAAGTGAAGATTTTAAGCATTCCACCTGAGAAGTACTGTCGCAAGACTGAAACTCAAAACATTAGACGGTCACAGAGATCAGCAGTGAAGCATGTTGTTTAATTCGATAACCCACGATAAATCTTAGCACTTCTTGCATATTTTCCTATTCGGAATTTACAGGTGTTGCATGGCTGTCTTTAGTTCGTGTTGTGAAATGTTAGGTTTATTCCGATAACGAACGTAAACCTTGTCCTTAATTATTTTAAGGAAATGTCTATCGATATTATAGATGAATGAGGATGAAGACAAGTCCTCATGACCCTTATGAAGTGGGCTACAGACGTGCTGCAAAATTTTCTACAATGGGATGCAATGATGGAAGTCGGAGCTAATCCCCTAAAAGATTGTTTAGTCCGGATAAGTGCCTGGAACTCGGCTCTTTGAAGTTGGAATTGCTAGTAATCGTCTATCATCATGAGACGGTGAATCTTTTATCTGTGATGTACTAACTACTCGTCAAGCGCGGAAATTTTTTAAGAAATTCAAGTTCTTACGTCCATTTCTTGGAGATCTGTGCTAAGTCGAAATAAGGTAGCTGTAGGGGAACCCTGTAGCTGAATAATTTGTGTTGTTTAAATCCCCCCCATCCTTGTG.The reference sequence used to design primersand a probe for the quantification of theRNA transcripts of CYTochrome B (CYTB) isreferenced in GENBANK® under the accessionnumber AF074871.1 (SEQ ID NO: 3), which is: (SEQ ID NO: 3)TATTTATGGAATTATGGTTCATTATCAGGACTGTGTTTAATTATACAGATTATTACGGGTGTGACTTTAGCTATGGATTATATACCTTCGATTGATTTAGCTTTCTTGAGTGTTGAACATATTATGTGAGATGTAAATTATGGTTGGTTGATTCGTTATATTCATAGTAATACGGCTTCTTTTTTCTTTCTGTTTGTTTATATTCATATTGCTTGAGGTATCTATTATGGATCTTATCGAACTCCCAGAATTCTCGTTTGGTCTATTGGTGTAGTTATCTTCTTAATTATGATTGTTACTGCTTTCTTGGGATATGTTCTGCCTTTTGGTCAAATGTCATTGTGGGGAGCGACTGTTATTACTAATTTGATGTCTGCTATACCTTGGATTGGTAATGATATTGTGAATTTTATTTGGGGTGGGTTCTCTGTTAATCATGCTACTCTGAATTGATTCTTCTCTTTACATTATTTATTGCCTTTTGTTTTATTGGCTTTAGTTGTTGCTCATTTAATCTCTTTACATGTTCATGGAAGTAGTAATCCTCTGGGTGTTACTGGTAATTCAGATCGTCTGCCTTTCCATCCCTATTTCTCATTTAAAGATTTAGTTACTGTTTTTTTATTTTTATTAGCTTTATGTTTCTTTGTGTTTTATGCTCCTAATGTCTTGGGACATAGTGATAATTATATTATGGCTAATCCTATGGCTACTCCTCCAAGTATTGTTCCTGAATGGTATCTTTTACCTTTCTATGCAATCTTGTGATCTATTTCGAATAAATTATTTGGAGTTGTGGCTATGTTAGCTGCTATTCTTATTCTTTTTGTTTTACCTCTTGTGGATTTATCTTGAATTTGAGGTTCTGCTTTTAGACCTCTTAGTAAATTCTTTTTTTGGATCTTTGTCACTAATTTCTTCTTGTTAATGTTTGTGGGTTGACAACATGTTGAAGAACCTTTTGTGACGCTTGGACAATATGCTACATTCTTCTATTTCTTCTATTTCTTAGTTGTTATTCGTCTGGTGGGTATTATT.The reference sequence used to design primersand a probe for the quantification of theRNA transcripts of the Beta TUBuline (BTUB)is referenced in GEN BANK® under theaccession number AF170964.1 (SEQ ID NO: 4), which is: (SEQ ID NO: 4)    1 ggcgcctctt tttggagcac cattagcggt gaacacggtc ttgatagcac tggcctgtaa   61 gcaatattgt aatactgcag tgtgtttgca gaggtgatta gaaatgccta taaggcagca  121 aaaaggcatt gaaaagactc caaagaagta caaagatgct ctgcaaacaa tctaaaaaca  181 tgcagtaata ctgcatgttt gcagtacttt ttttccaaaa cttatatttt tcagctatca  241 tggaacctct gatctccaac tcgaacggat gaatgtttat ttcaacgagg tttctacgga  301 aaaatgttta tagaatgtca gacatttatt ttaataggca tctggcggga aatacgtgcc  361 tcgtgcagta ctggttgatt tagagcccgg tacaatggat gcagtacgtt ctgggccatt  421 tgggaacctg tttcgaccag ataattttat ttttggtcaa tcaggtgcag gaaataactg  481 ggcaaaaggg cattatacag agggagcgga attggtagat actgtgttag atgtagttcg  541 tcgggaagcc gaagcatgtg attgcttgca aggattccag attacacatt cattaggtgg  601 tggaacgggt gcaggcatgg gaactttgct aatttcgaaa attcgagagg aatatccgga  661 tcggatgatg gcaacgtttt cagtggttcc ctcaccaaaa gtttccgata cagttgtaga  721 gccatataat gcaacattat cagtgcatgt gtgtttttaa gccattttta gaatgtatat  781 taatgaggag gggtagcaat tagttgaaaa ttccgatgaa acattctgta tcgacaatga  841 agcattatat gatattcgta tgcgtacatt aaaattgccg gatccaggat atggtgattt  901 gaatcatctt gtctcggcag taatgagtgg tattacaact tgtcttcgat ttcctggaca  961 actcaactcg gatttgcgta aattggccgt taatatggtg ccgtttcctc gtttgcactt 1021 tttcatggtt gggtttgctc cattaacaag cagtaagatg ctttaaacgt attctgaaat 1081 ggctgattgt tattctgtct agagggatca cattcatttc ggtcattgac agttcctgaa 1141 ttgactcagc aaatgtttga tgcaaagaat atgatggcag catcggatcc gagacatggt 1201 cgctatttaa ctgttgcagc gattttccgc ggtactgttt ccatgaagga ggttgaagat 1261 caaatgcata atgttcagca gaagaactct tcatattttg ttgaatggat tccaaacaat 1321 gtgcaaaccg cgctatgttc tattccacca cgtggtctca aaatgtcatc aacgtttatt 1381 ggcaattcaa catctattca ggaactattt aaacgtgtag gcgaccaatt tgctgca.The reference sequence used to design primersarid a probe for the quantification of theRNA transcripts of HSP70 is referenced inGEN BANK® under the accession numberDQ987621.1 (SEQ ID NO: 5), which is: (SEQ ID NO. 5)    1 gacggaaact cggggatcca gaagcgcaat cagatatgaa acattggcct tttaaagtta   61 taqacaaagg tcagaagcct tatattcagg ttgaatataa aggggatatt aaaacattta  121 cgccggagga gatttcatca atggtcctta caaaaatgaa ggaggtggca gaagcgtatc  181 ttgggactaa agtttccaat gccgttatca cggtcccagc atatttcaat gactcacagc  241 gacaggctac gaaagacgca ggattgattg caggattgaa tgttttacgt attatcaatg  301 aacctacagc agcagccatt gcatatggtc tagataagaa gacatcaaat gaaaagaatg  361 tgcttatttt tgatcttgga ggaggaactt ttgacgtatc gttattaact atcgaagagg  421 gaatttttga agtcaaagca accgcaggcg atacccattt gggaggagaa gattttgaca  481 atcgtcttgt aaaccacttc attgctgaac gcaaacacaa gaaagatctt tcagggaatg  541 cacgatctct tcgtcggctt cgaacagcat gtgagcgtgc taaacggact ctttcatcat  601 caacacagac gagtatagaa attgattcct tatttgaagg aattgattta tatacttcta  661 ttactcgtgc tcgatttgaa gaactttgtc aaggtctttt taggggaaca atggaaccag  721 ttgagaaagt tcttcgtgat tctaaaattg ataaatcaag tgttcatgaa attgtattgg  781 ttggtggttc tacgcgtatt ccgcgtattc agaaattggt ttgtgatttt tttaatggaa  841 aagagccaaa tagaacgatc aatccagatg aggctgttgc ctatggtgcg gcagttcaag  901 ttgctattct ttcaggagac acatcggaac aaactcaaga catactcttg cttgatgtgg  961 cgcctctctc aatgggt. The reference sequence used to design primersand a probe for the quantification of theRNA transcripts of COX1 is referenced inGENBANK® under the accession numberJX499143.K REGION: 16256 . . . 17836 (SEQ ID NO: 6), which is:(SEQ ID NO: 6) 16256 atgac16261 atgatggttg ttttcaacaa atgctaagga tatcggagtc ttgtacttga tctttgcact16321 tttttctgga atgttgggta cagcatattc agtattattg agaatggaat taacttcccc16381 aggtgttcag tatttacagg gtgataatca attgtataat gtaattttaa cgagtcatgc16441 gttgttaatg atattcttta tggttatgcc cggaatggta ggaggttttg gtaattggtt16501 ggttccagta atgattggag caccagatat ggcctttcca agattaaata atatctcctt16561 ctggttgtta ccgccttctc tgattctgtt aattgcttct tctcttctag aaggtggaag16621 tggtacaggt tggacttttt atccaccttt gtccagttta caaagtcatt cctcaggtgc16681 tgtcgatttg tctatcttta gtctacattc agcaggtatt agttctatgt tgggagctat16741 taattttatt actactgttc ttaatacttg agctcccggt atgactatgc ataaaattcc16801 attgtttgca tggtctatct ttgttactgc tatactgttg ttattgtcct tgccagtctt16861 agcaggaggt attactatgc tcttgacgga ttgaaatttt aatacttcct tctatgatgt16921 cgcaggagga ggggatccta tcctttatca acatctcttc tggttcttcg gacatccaga16981 agtttatatt ctgattattc caggatttgg tatcattagt catattattt ccactttctc17041 tggaaaacca gtattcggtt atttaggtat ggtttatgct atgttgtcaa ttggtgtctt17101 aggatttatt gtctggagtc atcatatgta ttcagtgggt ttagatgttg atacatgagc17161 ttattttact gctgctacta tgattattgg tgtacctact ggtattaaaa tcttctcttg17221 gattgctact atgtatggtg gtgtgattcg atttaataca cctatgctct ttgctatcgg17281 attccttttc ctttttactg tgggaggatt aacgggtatt gtcttgtcta atgcttcttt17341 agatgtggct ttacatgata cttattatgt tgtagctcat ttccattatg ttttatccat17401 gggtgcagtc tttgctctct tagcagcttg gtatttctgg tctccaaaaa ttttaggatt17461 gttctttgat gaaaaattag ggcatttgca tttctggact ctttttattg gagtgaattt17521 aacttttatg cctatgcatt tcttgggatt acagggtatg cccagatgaa ttcctgatta17581 tcctgatgct tttgctcagt ggaatcatat ctcaagttta ggtagtttga tttctgttgt17641 tgctactgtt gtttttattt attctatttt tgatcaattg atctctaaat gattggtacc17701 gatgaatcct tggtattctc ctgatttctt tgttagtcat acgaatttag aggattccaa17761 agcttgttcc ttagaatggg cattgatttc accaccagct ttccatgctt atactagttt17821 acctaaacaa gcttaa. The reference sequence used to design primersand a probe for the quantification of theRNA transcripts of NAD1 is referenced in GENBANK® under the accession numberJX499143.1, REGION: 29671 . . . 30672 (SEQ ID NO: 7), which is:(SEQ ID NO: 7) 29671 atgttaaatt gtattcaagt gggtattgtt29701 ttattacctg ttttgttaag tgtagctttt gtgacattag ctgaacgtaa agttatggga29761 tcgattcaac gacgtgtggg tcctaatgtt gtgggttatt atggtttgtt acaacctgca29821 gctgatgctt taaaattatt attaaaagaa actattattc ctatccattc gaataaagtg29881 ttgttcttct taggaccttc tattgcatta gtctttgctt taatgggttg gggtattatt29941 ccatggaatt caggtataac actttgggat tttgatttag gtattttatt tagtttagct30001 atttcttctt taggtgtgta tggtatttta attgggggtt gggcttctaa ttccaaatat30061 gctttattag gttccttgtg aagtactgct caattaatta gttatgaatt agttttaact30121 tcgattgttt ttgttgttgt tcttttatct ggttctttta attttactca cattattgaa30181 gaacaaaaag ctatttggtt tgttttgcct ttatttcctc tgttcatttt gttctttact30241 ggtgctttag cagaaacgaa ttgagctcct tttgatttgc cagaagctga atccgaatta30301 gttgctgggt ttatgactga gtattctgct gcgatctttg ttttcttctt cctagctgaa30361 tatgctaata ttattcttat ctctactcta gctgctattt tcttcttagg aggttattta30421 ttacctttcg agttgcattt cttgcctaat ggtttagatg ttctcgttca gggattactt30481 tctggtttga ttttaggttt gaaagttgct gggattattt tcctctttgt ttgggtttga30541 tctagcttcc ctagaatttg atatgatcaa ttgttagttc tatgttggac tgttctgtta30601 cctttgcttt ttgctcggat ttttctggtt ttagctattc ttttttcttt taattctttt30661 attcatttct ag. The reference sequence used to design primersand a probe for the quantification of theRNA transcripts of ATP9 is referenced in GENBANK® under the accession numberJX499143.1, REGION: 20225 . . . 20449 (SEQ ID NO: 8), which is:(SEQ ID NO. 8)20225 atgtta caagcagcta aagttattgg ttcagggtta gctacaattg gattagcagg20281 ggctggtatc ggtatcggtt tagttttcgg taatttacca gtagcgacaa gtcgaaatcc20341 ttcattgaaa ggacaactct tctcttatgc tatcttggga tttgctctag cagaagctac20401 tggtcttttc tgtttgatga tggctttcct tctgctatat gcagcttaa.

qRT-PCR Amplification

For each sample, the expression of the mtLSU, the CYTB, the BTUB, theHSP70, the COX1, the NAD1 and the ATP9 genes were tested (quantificationof RNA transcripts). All PCR reactions were performed on a LIGHTCYCLER®480 instrument (ROCHE DIAGNOSTICS; 2, Avenue du Vercors; BP 59; 38242MEYLAN CEDEX; FRANCE) in a final volume of 10 μL containing 0.2 μL ofEXPRESS SuperScript® III Mix for One-Step qRT-PCR (INVITROGEN™ by LIFETECHNOLOGIES™; 5791 Van Allen way; Carlsbad; CA 92008: U.S.A.), 1×EXPRESS SuperScript® III SuperMix Universal buffer (INVITROGEN™ by LIFETECHNOLOGIES™; 5791 Van Allen way; Carlsbad; CA 92008; U.S.A.), with 0.3μM of each primer, 0.1 μM of the probe and 2 μL of a 1:2 dilution ofRNA. The reaction consisted of a reverse transcription step at 50° C. 15min, followed by DNA polymerase activation at 95° C. 2 min and 45 cyclesof 95° C. 15 s and 60° C. 30 s.

The mtLSU (RNA) target was: SEQ ID NO: 9CACUGAAUAUCUCGAGGGAGUAUGAAAAUAUUUAUCUCAGAUAUUUAAUCUCAAAAUAACUAUUUCUUAAAAUAAAUAAUCAGACUAUGUGCGAUAAGGUAGAUAGUC GAAAGGGAAACAG.The cDN A reverse-transcript of the mtLSU target was (fragment 861-981from SEQ ID NO: 1): SEQ ID NO: 10 CACTGAATATCTCGAGGGAGTATGAAAATATTTATCTCAGATATTTAATCTCAAAATAACTATTCTTAAA ATAAATAATCAGACTATGTGCGATAAGGTAGATAGTCGAAAGGGAAACAG. Primers and probe used for the detectionof the targeted region of the mtLSU RNA were: PjF1: (SEQ ID NO: 11)5′-CACTGAATATCTCGAGGGAGTATGAA-3′ PjR1: (SEQ ID NO: 12)5′-CTGTTTCCCTTTCGACTATCTACCTT-3′ and the PjSL probe: (SEQ ID NO: 13)5′-TCGCACATAGTCTGATTAT-3′ under TAQMAN® format(FAM™ in 5′ and MGB® in 3′). FAM™ = 6-carboxy-fluorescein dyeMGB® = Minor Groove Binder® quencher A mtSSU (RNA) target can be:SEQ ID NO: 14 GCAAUGAUGGAAGUCGGAGCUAAUCCCCUAAAAGAUUGUUUAGUCCGGAUAAGUGCCUGGAACUCGGC UCUUUGAAGUUGGA.The cDNA reverse-transcript of thismtSSU target can be (fragment 1154-1235 from SEQ ID NO: 2):SEQ ID NO: 15 GCAATGATGGAAGTCGGAGCTAATCCCCTAAAAGATTGTTTAGTCCGGATAAGTGCCTGGAACTCGGCTCTT TGAAGTTGGA.Primers arid probe for the detection ofthis mtSSU RNA target region can be: Pj1154F: (SEQ ID NO: 16)5′-GCAATGATGGAAGTCGGAGC-3′. PJ1235R: (SEQ ID NO: 17)5′-TCCAACTTCAAAGAGCCGAGT-3′. and the Pj1190P probe: (SEQ ID NO: 18)5′- TGTTTAGTCCGGATAAGTGCCTGGA-3′ under TAQMAN® format (FAM™ in 5′and BHQ-1® in 3′). BHQ-1® = Black Hole Quencher®-1.Another mtSSU (RNA) target can be: SEQ ID NO: 19GGAUGCAAUGAUGGAAGUCGGAGCUAAUCCCCUAAAAGAUUGUUUAGUCCGGAUAAGUGCCUGGAACUCGGC UCUUUGAAGUUGGAAUUGCU.The cDNA reverse-transcript of this mtSSU target can be (fragment1150-1241 from SEQ ID NO: 2): SEQ ID NO: 20GGATGGAATGATGGAAGTCGGAGCTAATCCCCTAAAAGATTGTTTAGTCCGGATAAGTGCCTGGAACTCGGC TCTTTGAAGTTGGAATTGCT.Primers and probe for the detection ofthis mtSSU RNA target region can be: Pj1150F: (SEQ ID NO: 21)5′-GGATGCAATGATGGAAGTCGGA-3′, Pj1241R: (SEQ ID NO: 22)5′-AGCAATTCCAACTTCAAAGAGCC-3′, and the Pj1190P probe: (SEQ ID NO: 23)5′-TGTTTAGTCCGGATAAGTGCCTGGAAC-3′ under TAQMAN® format (FAM™ in 5′and BHQ-1® in 3′). Still another mtSSU (RNA) target can be:SEQ ID NO: 24 UCAUGACCCUUAUGAAGUGGGCUACAGACGUGCUGCAAAAUUUUCUACAAUGGGAUGCAAUGAUGGAAGUCG GAGC.The cDNA reverse-transcript of thismtSSU target can be (fragment 1098-1173 from SEQ ID NO: 2):SEQ ID NO: 25 TCATGACCCTTATGAAGTGGGCTACAGACGTGCTGCAAAATTTTCTACAATGGGATGCAATGATGGAAGTCG GAGC.Primers and probe for the detection ofthis mtSSU RNA target region can be: Pj1098F: (SEQ ID NO: 26)5′-TCATGACCCTTATGAAGTGGGC-3′, Pj1173R: (SEQ ID NO: 27)5′-GCTCCGACTTCCATCATTGC-3′. and the Pj1125P probe: (SEQ ID NO: 28)5′-ACGTGCTGCAAAATTTTCTACAATGGG-3′ under TAQMAN® format (FAM™ in 5′and BHQ® in 3′). The CYTB (RNA) target was: SEQ ID NO: 29CUCCCAGAAUUCUCGUUUGGUCUAUUGGUGUAGU UAUCUUCUUAAUUAUGAUUGUUACUGCUUUCUUGGGAUAUGUUCUGCCUUUUGGUCAAAUGUCAUUGU GGG.The cDNA reverse-transcript of the CYTB target was (fragment 242-346from SEQ ID NO: 3): SEQ ID NO: 30 CTCCCAGAATTCTCGTTTGGTCTATTGGTGTAGTTATCTTCTTAATTATGATTGTTACTGCTTTCTTGGG ATATGTTCTGCCTTTTGGTCAAATGTCATTGTGGG.Primers and probe used for the detectionof the targeted region of the CYTB RNA were: CYTB_Pj242F:(SEQ ID NO: 31) 5′-CTCCCAGAATTCTCGTTTGG-3′ CYTB_Pj346R: (SEQ ID NO: 32)5′-CCCACAATGACATTTGACCA-3′ and the CYTB_Pj301P probe: (SEQ ID NO: 33)5′-CTTTCTTGGGATATGTTCTGCC-3′ under TAQMAN® format (FAM™ in 5′and TAMRA™ in 3′). TAMRA™ = carboxytetramethylrhodamine fluorescent dye.Primers and probe used for the detection of STUB RNA were: BTUB_PJ766F:(SEQ ID NO: 34) 5′-CCATTAACAAGCAAGGGATCAC-3′ BTUB_Pj861R:(SEQ ID NO: 35) 5′-CGATGCTGCCATCATATTCTT-3′ and the BTUB_Pj795P probe:(SEQ ID NO: 36) 5′-TCGGTCATTGACAGTTCCTGAA-3′under TAQMAN® format (FAM™ in 5′ and TAMRA™ in 3′).Primers and probe used for the detection of HSP70 RNA were:HSP70_PJ126F: (SEQ ID NO: 37) 5′-GGAGATTTCATCAATGGTCCTT-3′ HSP70_Pj202R(SEQ ID NO: 38) (5′-CGGCATTGGAAACITIAGTCC-3′ and the HSP70_PJ157P probe:(SEQ ID NO: 39) 5′-AAGGAGGTGGCAGAAGCGT A-3′under TAQMAN® format (FAM™ in 5′ and TAMRA™ in 3′).An aliquot of a sample with a definedquantification was used in each PCR to be run as an internal control andto measure reproducibility. For mtLSU, CYTB, BTUB and MSP70, theCq values ± SD were 24.1 ± 0.3, 23.6 ± 0.3,32.5 ± 0.3, 29.0 ± 0.2, respectively. Primers and probe used for thedetection of COX1 RNA were: COX1_Pj228F: (SEQ ID NO: 40)5′-AGGTTTTGGTAATTGGTTGGTTCC-3′ COX1_PJ324R: (SEQ ID NO: 41)5′-AGAAGGCGGTAACAACCAGAA-3′ and the COX1_Pj261P probe: SEQ ID NO: 42)5′-TGGAGCACCAGATATGGCCTTTCCAAGA-3′; under TAQMAN® format (FAM™ in 5′and BHQ-1™ in 3′). BHQ-1™ = Black Hole Quencher®-1.Primers and probe used for the detection of NAD1 RNA were: NAD1_Pj579F:(SEQ ID NO: 43) 5′-AGCAGAAACGAATTGAGCTCCT-3′ NAD1_Pj664R:(SEQ ID NO: 44) 5′-TCGCAGCAGAATACTCAGTCAT-3′ and the NAD1_PJ608P probe:(SEQ ID NO: 45) 5′-TGCCAGAAGCTGAATCCGAATTAGTTGC-3′under TAQMAN® format (FAM™ in 5′ and BHQ-1™ in 3′).Primers and probe used for the detection of ATP9 RNA were: ATP9_PJ25F:(SEQ ID NO: 46) 5′-GGTTCAGGGTTAGCTACAATTGGA-3′ ATP9_Pj118R:(SEQ ID NO: 47) 5′-AAGGATTTCGACTTGTCGCTACT-3′ and the ATP9_Pj52P probe:(SEQ ID NO: 48) 5′-GCAGGGGCTGGTATCGGTATCGGTTTAG-3′under TAQMAN® format (FAM™ in 5′ and BHQ-1™ in 3′).

Gene Expression Determination

For determination of the gene expression level of the different samples,all quantification data (Cq) were normalized compared to the BTUBexpression. Experimental calibration curves allowed determination of thePCR efficiency (e) that was required to determine gene expression foreach PCR. At the end, the expression of CYTB was compared to that ofmtLSU gene without taking into account BTUB expression with modificationof the formula of Pfaffl 2001 as:

CYTB/mtLSU ratio=E(CYTB)^(−Cq(CYTB)) /E(mtLSU)^(−Cq(mtLSU))

The real-time PCR efficiency (E) of one cycle in the exponential phasewas calculated according the formula E=10^([−1/slope]) as described inPfaffl 2001. The real-time PCR efficiency values for CYTB, mtLSU, BTUBand HSP70 are reported in Table 8.

Data Analysis

Correlation with clinical data was performed only with one sample perpatient. Statistical analyses were performed with PRISM® v5.0 (GraphPADSoftware Inc.; 7825 Fay Avenue; Suite 230: LA JOLLA, Calif. 92037,U.S.A.).

Results

Detection of RNA in BALF

From all 200 samples, mtLSU RNA PCR was compared to the miLSU DNA PCRperformed as a routine test. From the 200 samples, 34 (17%) were bothpositive and 148 (74%) were both negative with RNA and DNA PCR; cf.Table 2 below.

TABLE 2 Distribution of the number of samples regarding DNA and RNAmtLSU PCR Positive RNA Negative RNA Number of samples mtLSU PCR mtLSUPCR Total Positive DNA mtLSU PCR 34 5 39 Negative DNA mtLSU PCR 13 148161 Total 47 153 200

In 5 (2.5%) samples, mtLSU DNA but not RNA was detected, whereas in 13samples, mtLSU RNA was detected but not DNA (cf. Table 2 above). RNAdetection (n=47) is more sensitive than DNA detection (n=39) in BALF.

In addition, the fungal load was significantly higher with RNA than withDNA detection (FIG. 1, paired t-test: p<0.0001). RNA detection gave a 10fold higher detection than DNA with a mean ΔCq (DNA-RNA) at 3.577 (95%confidence interval: 2.681-4.473).

In the 47 samples positive for mtLSU rRNA, CYTB, BTUB and HSP70 mRNAwere detected in 31 (66%), 32 (68%) and 32 (68%) samples, respectively.

Clinical Probability of PCP Classification

From the 200 BALF prospectively collected from 192 patients, 2 samples(2 patients) harboring a positive DNA PCR were excluded because of lackof clinical data.

At the end, a total of 49 patients (50 samples) with either RNA or DNAdetection were investigated for classification. Eighteen patients wereconsidered as PCP (proven PCP in 14 patients, probable PCP in 1 patientand possible PCP in 3 patients) and 31 patients as no PCP.

No difference in the repartition of the different groups of disease wasobserved in patients with and without PCP (chi-2, p=0.063, cf. Table 3below).

TABLE 3 Distribution of the PCP and no PCP patients according todifferent groups of diseases Background PCP no PCP p Hematologicalmalignancies 7 13 0.063 HIV positive 8 4 SOT 1 2 others 2 5 No ID 0 7Total 18 31

In the PCP patients, 14 samples (14 patients) were diagnostic samplesand 5 samples (4 patients) were not performed as diagnostic samples butto search for other etiology of a persistent or recently acquiredpneumonia after PCP diagnosis and more than 15 days of cotrimoxazoletreatment (analyzed apart for the others specimens and called follow-upsamples). Patients with PCP were composed of hematological malignancies(7/14, 50%), HIV patients (8/14, 57%), solid organ transplant (SOT)(1/14, 7%) and other background (2/14, 14%). Immunofluorescence waspositive in 8/14 (57%) patients and negative in 6/14 (43%) patients.Based on immunofluorescence results, sensitivity and specificity were0.57 (95% CI, 0.289-0.823) and 1.00 (95% CI, 0.888-1.000), respectively.The ROC curve analysis of the quantification results (mtLSU RNA PCR)allowed determination of the best quantification cycle (Cq) thresholdbetween 30.49 and 31.78 (FIGS. 2A and 3B). Based on the quantificationresults, optimal sensitivity and specificity were 0.812 (95% CI,0.543-0.959) and 0.960 (95% CI, 0.796-0.999) for diagnostic samples(n=41, FIG. 2A and Table 7) and 0.650 (94% CI 0.408-0.846) and 0.961(95% CI, 0.804-0.999) for diagnostic and follow-up samples (n=46, FIG.2B and Table 7).

Variable CYTB/mtLSU Ratio in Different Categories of Patients

No PCP patient was recorded in the 16 samples with positive mtLSU RNAand negative CYTB RNA PCR and in the 152 samples with negative mtLSU andCYTB RNA PCR (cf. Table 6 below).

TABLE 6 Repartition of the samples in the different categories ofsamples regarding the expression of CYTB and mtLSU Clinicalclassification PCP w Rx Categories of samples PCP 15 days no PCPCYTB/mtLSU > 1.66 1 5 9 CYTB/mtLSU < 1.27 13 0 2 No CYTB 0 0 16 NoCYTB/No mtLSU 0 0 152

The ROC curve analysis of the CYTB/mtLSU ratios was performed and showedthat a threshold between 1.27 and 1.66 allowed the higher likelihoodratio (LR: 12.96) (cf. Table 4 below, cf. FIGS. 2A and 3B).

TABLE 4 ROC curve data of the PCP Xpress test based on diagnosticsamples (n = 41) Cutoff CYTB/mtLSU Likelihood ratio Sensitivity % 95% CISpecificity % 95% CI ratio −156.9 100.0 87.23 to 100.0 7.143 0.1807 to33.87  1.08 −3.985 100.0 87.23 to 100.0 14.29 1.779 to 42.81 1.17 −2.86496.30 81.03 to 99.91 14.29 1.779 to 42.81 1.12 −2.386 96.30 81.03 to99.91 21.43 4.658 to 50.80 1.23 −2.191 96.30 81.03 to 99.91 28.57 8.389to 58.10 1.35 −1.992 96.30 81.03 to 99.91 35.71 12.76 to 64.86 1.50−1.926 96.30 81.03 to 99.91 42.86 17.66 to 71.14 1.69 −1.903 96.30 81.03to 99.91 50.00 23.04 to 76.96 1.93 −1.763 92.59 75.71 to 99.09 50.0023.04 to 76.96 1.85 −1.546 92.59 75.71 to 99.09 57.14 28.86 to 82.342.16 −1.398 92.59 75.71 to 99.09 64.29 35.14 to 87.24 2.59 −1.279 92.5975.71 to 99.09 71.43 41.90 to 91.61 3.24 −1.222 92.59 75.71 to 99.0978.57 49.20 to 95.34 4.32 0.02900 92.59 75.71 to 99.09 85.71 57.19 to98.22 6.48 1.472 92.59 75.71 to 99.09 92.86 66.13 to 99.82 12.96 1.90988.89 70.84 to 97.65 92.86 66.13 to 99.82 12.44 2.544 85.19 66.27 to95.81 92.86 66.13 to 99.82 11.93 3.959 81.48 61.92 to 93.70 92.86 66.13to 99.82 11.41 5.402 77.78 57.74 to 91.38 92.86 66.13 to 99.82 10.896.060 74.07 53.71 to 88.89 92.86 66.13 to 99.82 10.37 8.202 70.37 49.82to 86.25 92.86 66.13 to 99.82 9.85 10.11 66.67 46.04 to 83.48 92.8666.13 to 99.82 9.33 10.96 62.96 42.37 to 80.60 92.86 66.13 to 99.82 8.8114.93 59.2.6 38.80 to 77.61 92.86 66.13 to 99.82 8.30 59.02 59.26 38.80to 77.61 100.0 76.84 to 100.0

After addition of the 5 follow-up samples, a ratio between the samerange allowed the higher likelihood ratio (LR: 13.13) (cf. Table 5below, cf. FIGS. 2B and 3B).

TABLE 5 ROC curve data of the PCP Xpress test based on diagnostic (n =41) and follow up (n = 5) samples Cutoff CYTB/mtLSU Likelihood ratioSensitivity % 95% CI % 95% CI ratio 0.1085 100.0 89.11 to 100.0 7.1430.1807 to 33.87  1.08 0.2585 100.0 89.11 to 100.0 14.29 1.779 to 42.811.17 0.3570 100.0 89.11 to 100.0 21.43 4.658 to 50.80 1.27 0.4190 96.8883.78 to 99.92 21.43 4.658 to 50.80 1.23 0.4585 96.88 83.78 to 99.9228.57 8.389 to 58.10 1.36 0.5025 96.88 83.78 to 99.92 35.71 12.76 to64.86 1.51 0.5195 96.88 83.78 to 99.92 42.86 17.66 to 71.14 1.70 0.526096.88 83.78 to 99.92 50.00 23.04 to 76.96 1.94 0.5705 96.88 83.78 to99.92 57.14 28.86 to 82.34 2.26 0.6490 96.88 83.78 to 99.92 64.29 35.14to 87.24 2.71 0.7170 96.88 83.78 to 99.92 71.43 41.90 to 91.61 3.390.7835 93.75 79.19 to 99.23 71.43 41.90 to 91.61 3.28 0.8185 93.75 79.19to 99.23 78.57 49.20 to 95.34 4.38 1.050 93.75 79.19 to 99.23 85.7157.19 to 98.22 6.56 1.473 93.75 79.19 to 99.23 92.86 66.13 to 99.8213.13 1.745 90.63 74.98 to 98.02 92.86 66.13 to 99.82 12.69 1.989 87.5071.00 to 96.49 92.86 66.13 to 99.82 12.25 2.545 84.38 67.21 to 94.7292.86 66.13 to 99.82 11.81 3.025 81.25 63.56 to 92.79 92.86 66.13 to99.82 11.38 3.412 78.13 60.03 to 90.72 92.86 66.13 to 99.82 10.94 4.34775.00 56.59 to 88.54 92.86 66.13 to 99.82 10.50 5.402 71.88 53.25 to86.25 92.86 66.13 to 99.82 10.06 6.060 68.75 49.99 to 83.88 92.86 66.13to 99.82 9.63 7.766 65.63 46.81 to 81.43 92.86 66.13 to 99.82 9.19 9.66962.50 43.69 to 78.90 92.86 66.13 to 99.82 8.75 10.11 59.38 40.64 to76.30 92.86 66.13 to 99.82 8.31 10.79 56.25 37.66 to 73.64 92.86 66.13to 99.82 7.88 11.64 53.13 34.74 to 70.91 92.86 66.13 to 99.82 7.44 14.9350.00 31.89 to 68.11 92.86 66.13 to 99.82 7.00 59.02 50.00 31.89 to68.11 100.0 76.84 to 100.0

Without treatment, all IF positive samples had a ratio <1.27. After 15days of cotrimoxazole in patients that had an IF-positive sample, CYTBand mtLSU could be amplified and the ratio was >1.66. In IF negativesamples, ratio <1.27 and >1.66 were observed corresponding to patientwith PCP but with negative IF or to colonized patients.

After clinical classification, samples from PCP patients had mostly aratio <1.27 (13/14, 92.9%) whereas those from patients treated withcotrimoxazole >15 days (5/5, 100%) and those from patients without PCPhad mostly a ratio >1.66 (9/11, 81.9%) (cf. Table 6 above, cf. FIG. 3B).

Performance of the PCP Xpress Test

The diagnostic performances of our test were then calculated based ondifferent categories of samples. Taking into account the samples forwhich a ratio is determinable (positive CYTB and mtLSU RNA PCR, n=25),with a CYTB/mtLSU ratio threshold at 1.5 (threshold between ]1.27 to1.66[), sensitivity, specificity, Positive predictive value (PPV) andnegative predictive value (NPV) and the likelihood ratio (LR) were0.867, 0.900, 0.929, 0.818, 8.667 (cf. Table 7 below).

TABLE 7 Sensitivity, specificity, positive predictive and negativepredictive values, likelihood ratio of the PCP Xpress and RNA mtLSU qPCRtest in diagnostic and diagnostic and follow-up samples SamplesDiagnostic and Diagnostic and Follow up Diagnostic and Diagnostic andfollow up CYTB and mtLSU positive CYTB and mtLSU positive mtLSU positiveand mtLSU positive (n = 25) (n = 30) (n = 41) (n = 46) Test used PCPXpress RNA qPCR PCP Xpress RNA qPCR PCP Xpress RNA qPCR PCP Xpress RNAqPCR Sensitivity 0.8667 0.8667 0.8667 0.6842 0.8667 0.8125 0.8667 0.6500[95% CI] [0.5954 to [0.5954 to [0.5954 to [0.4345 to [0.5954 to [0.5435to [0.5954 to [0.4078 to 0.9834] 0.9834] 0.9834] 0.8742] 0.9834] 0.9595]0.9834] 0.8461] Specificity 0.9000 0.9000 0.9333 0.9091 0.9615 0.96000.9677 0.9615 [95% CI] [0.5550 to [0.5550 to [0.6805 to [0.5872 to[0.8036 to [0.7965 to [0.8330 to [0.8036 to 0.9975] 0.9975] 0.9983]0.9977] 0.9990] 0.9990] 0.9992] 0.9990] Positive 0.9286 0.9286 0.92860.9286 0.9286 0.9286 0.9286 0.9286 Predictive [0.6613 to [0.661.3 to[0.6613 to [0.6613 to [0.6613 to [0.6613 to [0.6613 to [0.6613 to Value[95% CI] 0.9982] 0.9982] 0.9982] 0.9982] 0.9982] 0.9982] 0.9982] 0.9982]Negative 0.8182 0.8182 0.8750 0.6250 0.9259 0.8889 0.9375 0.7813Predictive [0.4822 to [0.4822 to [0.6165 to [0.3543 to [0.7571 to[0.7084 to [0.7919 to [0.6003 to Value [95% CI] 0.9772] 0.9772] 0.9845]0.8480] 0.9909] 0.9765] 0.9923] 0.9072] Likelihood 8.667 8.667 13.007.526 22.53 20.31 26.87 16.90 Ratio Samples All diagnostic samples (n =193) All (n = 198) Test used PCP Xpress RNA qPCR PCP Xpress RNA qPCRSensitivity 0.8667 0.8125 0.8667 0.6500 [95% CI] [0.5954 to 0.9834][0.5435 to 0.9595] [0.5954 to 0.9834] [0.4078 to 0.8461] Specificity0.9944 0.9944 0.9945 0.9944 [95% CI] [0.9691 to 0.9999] [0.9689 to0.9999] [0.9699 to 0.9999] [0.9691 to 0.9999] Positive 0.9286 0.92860.9286 0.9286 Predictive [0.6613 to 0.9982] [0.6613 to 0.9982] [0.6613to 0.9982] [0.6613 to 0.9982] Value [95% CI] Negative 0.9288 0.98320.9891 0.9620 Predictive [0.9602 to 0.9986] [0.9518 to 0.9965] [0.9613to 0.9987] [0.9232 to 0.9846] Value [95% CI] Likelihood 154.3 143.8158.6 115.7 Ratio PCP Xpress: CYTB/mtLSU threshold between ]1.27 and1.66[ qPCR RNA mtLSU: Cq threshold at ]30.49 and 31.78[

If the 16 samples with a negative CYTB expression were added with aCYTB/mtLSU ratio threshold at 1.5 (threshold between]1.27 to 1.66[),sensitivity, specificity. PPV and NPV and LR were 0.867, 0.961, 0.929,0.926, 22.53 (cf. Table 7 above). If all diagnostic samples wereconsidered, with a threshold of CYTB/mtLSU ratio at 1.5 (thresholdbetween]1.27 to 1.66[), sensitivity, specificity, PPV and NPV and LRwere 0.867, 0.994, 0.929, 0.989, 154.3 (cf. Table 7 above). If follow-upsamples were included, in each category of samples, the likelihood ratiowas higher than with diagnostic samples alone (cf. Table 7 above).Overall, likelihood ratios were higher (LR=158.6) with PCP Xpress thanwith mtLSU RNA quantification (cf. Table 7 above).

Testing Gene Expression for Other Gene (HSP70, BTUB, COX1, NAD1, ATP9)Compared to mtLSU

HSP70 gene was tested because its mRNA was one of the most abundanttranscripts found in a transcriptome analysis of Pneumocystis cariniiduring a fulminate infection in a rat model of pneumocystosis. The BTUBgene was used as a reference gene and also tested in comparison to mtLSUOther mitochondrial genes were also investigated: COX1, NAD1 and ATP9.

The BTUB and HSP70 gene expression were tested in all samples inparallel to CYTB and mtLSU, COX1, NAD1, and ATP9 were tested in 9positive samples (4 recovered from PCP patients; and 5 recovered frompatients without PCP). ATP9 was not enough expressed to be used as adiagnostic marker.

For each gene, the ratio compared to mtLSU was calculated as describedabove.

The HSP70 and BTUB ratio in our study gave maximum likelihood ratios of5.83 and 9.69, respectively. These values were lower than for CYTB (cf.FIG. 4). No other ratio (CYTB vs. BTUB, mtLSU vs. BTUB, HSP70 vs. BTUB,HSP70 vs. CYTB) gave accurate discrimination between PCP and non-PCPsamples. In addition, it was not possible to see any differences in theCOX1 and NAD1 ratios in PCP and non-PCP samples (cf. Table 8 below).

TABLE 8 Gene expression and ratio to mtLSU obtained for 9 samples (4from PCP and 5 from non PCP patients) for the BTUB, HSP70, NAD1, COX1and CYTB genes BTUB | HSP70| NAD1| COX1| CYTB| BTUB mtLSU HSP70 mtLSUNAD1 mtLSU COX1 mtLSU CYTB mtLSU mtLSU Cq ratio Cq ratio Cq ratio Cqratio Cq ratio Cq Clinical PCR efficacy classification 1.975 1.94 2* 2*1.973 1.924 Sample 17 PCP 23.145 0.01 21.69 0.03 17.555 0.26 17.56 0.2616.885 0.52 16.545 Sample 21 PCP 30.03 0.02 28.825 0.07 26.73 0.13 26.730.13 25.17 0.53 25.16 Sample 30 PCP 28.82 0.01 23.155 0.57 24.68 0.1024.68 0.10 23.505 0.30 22.585 Sample 51 PCP 32.59 0.02 29.565 0.28 30.330.07 30.33 0.07 28.225 0.43 28.01 Sample 6 No PCP 38.73 0.09 38.28 0.2336.54 0.24 36.54 0.24 32.81 4.98 36.525 Sample 9 No PCP no na 37.51 0.0834.66 0.17 34.66 0.17 32.035 1.66 34.045 Sample 16 No PCP 37.44 0.0234.925 0.21 33.81 0.16 33.81 0.16 32.185 0.75 32.98 Sample 27 No PCP34.57 0.01 32.755 0.09 31.625 0.07 31.63 0.07 29.725 0.41 29.51 Sample57 No PCP 35.74 0.50 no na 36.4 0.20 36.4 0.20 31.13 11.82 36.1 *PCRefficacy was not calculated for NAD1 and COX1 gene, and was thereforefixed at 2. no = not detected na = not applicable

Example 2: Addition of an Internal Control as Control of RNA Extractionand/or Purification

An artificial or exogenous RNA can be added to the sample prior to theextraction and/or purification step. Such an artificial or exogenous RNAis known as an Internal Extraction Control RNA (IECR).

IECR can be an artificial cell containing calibrated RNA. Following RNAextraction and in parallel to testing the target genes (CYTB and mtLSU),the presence and the quantity of the control IECR, will be tested uponaddition in dedicated mix, and specific primers in a specific well.Signal derived from the Internal Control RNA confirms the success of theextraction step and is also used to determine the presence of inhibitorsin the RNA sample. IECR contains a sequence that had no significantknown homology to any published sequence and should not interfere withthe detection of the sample RNA (human and fungi). A negative controlreaction may also be performed.

Examples of IECR include:

-   -   the RNA extraction control commercialized by BIOLINE (BIOLINE        USA Inc.; 305 Constitution Dr.; TAUNTON; MA 027080; U.S.A.)        under catalog number BIO-38040 or BIO-35040,    -   the AMBION® ERCC RNA Spike-In Controls, which are commercialized        by LIFE TECHNOLOGIES S.A.S. (route de l'orme des merisiers;        Immeuble Discovery—Zone Technologique; 91190 SAINT AUBIN,        FRANCE), under catalog number 4456740, and    -   the RNA Internal Control, which is commercialized by QIAGEN®        (QIAGEN® France S.A.S.; 3, avenue du Canada; LP 809; 91974        COURTABOEUF CEDEX; FRANCE) under catalog number 211492.

Alternatively to the introduction of an artificial or exogenous RNAprior to the extraction and/or purification step, the control can beperformed by detecting that a human gene is still present after saidextraction and/or purification step. Examples of suitable human genesare known in the art and include constitutive genes, such as the humanalbumin (ALB) gene or the human TATA Box binding protein (TBP).

Said human gene can be detected using a probe, more particularly aprimer pair and a (real-time) probe, which specifically detect saidhuman gene.

Examples of primer pair and (real-time) probe for the human albumin(ALB) gene include

ALB Hs_10F (SEQ ID NO: 49) TCGTTACACCAAGAAAGTACCCC; ALB_Hs_89R(SEQ ID NO: 50) TGCTGCCCACTTTTCCTAGG; ALB_Hs_34P (SEQ ID NO: 51)AGTGTCAACTCCAACTCTTGTAGAGGT.

Examples of primer pair and (real-time) probe for the human TATA Boxbinding protein (TBP) include

TBP_Hs_107F (SEQ ID NO: 52) TGGCGTGTGAAGATAACCCA; TBP_Hs_204R(SEQ ID NO: 53) CGCTGGAACTCGTCTCACTA; and TBP_Hs_142P (SEQ ID NO: 54)TGCTGAGAAGAGTGTGGTGGAGATGC; or TBP_Hs_73F (SEQ ID NO: 55)ATCTTTGCAGTGACCCAGCA; TBP_Hs_169R (SEQ ID NO: 56) GAGCATCTCCAGCACACTCT;and TBP_Hs_93R (SEQ ID NO: 57) GCATCACTGTTTCTTGGCGTGTGAAG

Example 3: Alternate CYTB Probes and Primers

The CYTB (cDNA) probe that was used in Example 1 above was the probe ofSEQ ID NO: 33 under TAQMAN® format, using the FAM™ fluorophore in 5′ andthe TAMRA™ quencher in 3′.

Alternatively to the TAMRA® quencher, a Black-Hole Quencher®-1 (BHQ®1)was successfully used. With this alternate quencher, the efficiency ofthe simplex RT-PCR was of 1.94.

The simplex RT-PCR efficiency was of 1.92 for mtLSU (primers and probeof SEQ ID NOs: 11-13 as described in Example 1).

The simplex RT-PCR efficiency was of 1.95 for mtSSU (primers and probeof SEQ ID NOs: 26-28 as described in Example 1).

Each simplex RT-PCR was performed as described in Example 1, i.e., on aLIGHTCYCLER® 480 instrument (ROCHE DIAGNOSTICS; 2, Avenue du Vercors; BP59; 38242 MEYLAN CEDEX; FRANCE) in a final volume of 10 μL containing0.2 μL of EXPRESS SuperScript® III Mix for One-Step qRT-PCR (INVITROGEN™by LIFE TECHNOLOGIES™: 5791 Van Allen way; Carlsbad: CA 92008; U.S.A.),1× EXPRESS SuperScript® III SuperMix Universal buffer (INVITROGEN™ byLIFE TECHNOLOGIES™; 5791 Van Allen way; Carlsbad; CA 92008; U.S.A.),with 0.3 μM of each primer, 0.1 μM of the probe and 2 μL of a 1:2dilution of RNA. The reaction consisted of a reverse transcription stepat 50° C. 15 min, followed by DNA polymerase activation at 95° C. 2 minand 45 cycles of 95° C. 15 s and 60° C. 30 s.

The nucleotide sequence of SEQ ID NO: 33 (CYTB cDNA probe) can bemodified to replace at least one nucleotide by its Locked Nucleic Acid(LNA™) version (EXIQON™ Inc. 14 F Gill Street Woburn Mass. 01801U.S.A.).

For example, at least one of the T. A and G nucleotides of the sequenceof SEQ ID NO: 33 can be replaced by a LNA™-T, LNA™-A or LNA™-G,respectively.

For example, one to five nucleotides of the sequence of SEQ ID NO: 33can (each) be replaced by their (respective) LNA™ version.

For example, one to five of the T, A and G nucleotides of the sequenceof SEQ ID NO: 33 can (each) be replaced by their (respective) LNA™counterpart, i.e., a LNA™-T, LNA™-A or LNA™-G, respectively.

For example, the nucleotide sequence of SEQ ID NO: 33(CTT-TCT-TGG-GAT-ATG-TTC-TGC-C) can be modified intoCT8-TCT-8GG-G5T-ATG-8TC-T7C-C, wherein 8=LNA™-T, 5=LNA™-A and 7=LNA™-G(SEQ ID NO: 58) [the sequence complementary to SEQ ID NO: 58 beingG-G6A-GA5-CAT-A8C-CC5-AGA-5AG (SEQ ID NO: 59), wherein 8=LNA™-T,5=LNA™-A, 7=LNA™-G and 6=LNA™-C].

Such LNA modifications are intended to increase the specificity of thenucleotide sequence (i.e., in the case of SEQ ID NO: 33 or thecomplementary sequence thereof, to increase the specificity of the CYTBcDNA probe).

The CYTB forward primer that was used in Example 1 above was the primerof sequence SEQ ID NO: 31. Alternatively, the nucleotide sequence of SEQID NO: 31 (CYTB_Pj242F: 5′-CTC-CCA-GAA-TTC-TCG-TTT-GG-3′) can bemodified into CTC-CCA-GAA-TTC-TMG-TTT-GG, wherein M=C or A (SEQ ID NO:60) according to the IUPAC nucleotide code.

Such degenerated primer is intended to allow the detection and thequantification of CYTB mRNA in a sample from a patient having, in thisgenome, either a C or A at the position 255 of the nucleotide sequenceSEQ ID NO: 3 corresponding to CYTB gene.

Example 4: Alternate Ratio (Ratio mtSSU/mtLSU)

Bronchoalveolar lavage (BAL) fluid samples of 18 patients were analyzedfor detection and quantification of the RNA transcripts of mtSSU andmtLSU [twelve non-PCP patients that are P. pneumonia carriers; and sixPCP patients, who did not receive any anti-PCP treatment or who havereceived an anti-PCP treatment for at most 15 days].

All samples were positive for both RNA transcripts (mtSSU and mtLSU).

mtLSU RT-PCR was performed as described in Example 1 above (with themtLSU primers of SEQ ID NOs: 11-12 and the probe of SEQ ID NO: 13).

mtSSU RT-PCR was performed as described in Example 1 above (with themtSSU primers of SEQ ID NOs: 26-27 and the probe of SEQ ID NO: 28).

Quantification of mtSSU and of mtLSU:

mtSSU gene gives significantly better cycles results than mtLSU with amedian of 27.90 [C195% 24.39-28.55] compared to 30.00 [C195%26.51-31.36], respectively (p<0.001). Please see FIG. 5.

mtSSU/mtLSU Ratio:

The mtSSU/mtLSU RNA ratio allows discrimination between PCP and carriage(the optimal ratio being of 2.7).

A ratio from 3.1 to 3.3 would lead to 100% sensitivity but with a lowerspecificity (75% at 3.1 and 66.6% at 3.3). However, if the purpose wereto allow PCP diagnosis together with identifying the patients withcarriage, a ratio of 3.1 to 3.3 would be optimal to avoidmisidentification of PCP patients who needs to be treated for PCP.

The comparison of the ROC curves obtained with mtLSU or mtSSUquantification (Cycles) alone gave for both a maximal likelihood ratioat 6 for both. The mtSSU/mtLSU ratio gave the best result (likehoodratio at 10 for ratio of 2.7). Please see FIG. 6.

FIG. 7 shows the distribution of the mtSSU/mtLSU RNA ratio values in thePCP patients and in the carrier patients.

FIG. 8 shows the distribution of quantification values (cycles) of theRNA transcripts of the mtSSU et mtLSU genes in the PCP patients and inthe carrier patients.

BIBLIOGRAPHIC REFERENCES

-   Alanio et al. 2011. Real-time PCR assay-based strategy for    differentiation between active Pneumocystis jirovecii pneumonia and    colonization in immunocompromised patients. Clin Microbiol Infect    2011; 17: 1531-7.-   Pfaffl 2001. A new mathematical model for relative quantification in    real-time RT-PCR. Nucleic Acids Res 2001; 29: e45.-   Wang et al. 2009. RNA-Seq: a revolutionary tool for transcriptomics.    Nat. Rev. Genet. 2009 January; 10(1): 57-63.

1-33. (canceled)
 34. A kit suitable for diagnosing or predictingPneumoCystis Pneumonia (PCP) in a human patient, who is a Pneumocystisjirovecii carrier, or for determining or predicting the efficacy of adrug or treatment against PCP in a human patient, who is a Pneumocystisjirovecii carrier, wherein said kit comprises a reverse transcriptase, apolymerase, and oligonucleotides; wherein said oligonucleotides comprisea first primer pair and a second primer pair and/or a first probe and asecond probe; wherein said first primer pair and/or said first probespecifically hybridizes to the cDNA reverse transcripts of the RNAtranscripts of a first P. jirovecii mitochondrial gene; wherein saidsecond primer pair and/or said second probe specifically hybridizes tothe cDNA reverse transcripts of the RNA transcripts of a second P.jirovecii mitochondrial gene; and wherein the first and the second P.jirovecii mitochondrial genes are different.
 35. The kit of claim 34,wherein the first mitochondrial gene codes for the Cytb protein.
 36. Thekit of claim 34, wherein the first mitochondrial gene transcribes into aP. jirovecii ribosomal RNA.
 37. The kit of claim 35, wherein the secondmitochondrial gene transcribes into a P. jirovecii ribosomal RNA. 38.The kit of claim 36, wherein the second mitochondrial gene transcribesinto a P. jirovecii ribosomal RNA.
 39. The kit of claim 36, wherein thefirst mitochondrial gene is the P. jirovecii mitochondrial SmallSub-Unit (mtSSU) gene.
 40. The kit of claim 37, wherein the secondmitochondrial gene is the mitochondrial P. jirovecii Large Sub-Unit(mtLSU) gene.
 41. The kit of claim 38, wherein the second mitochondrialgene is the mitochondrial P. jirovecii Large Sub-Unit (mtLSU) gene. 42.The kit of claim 35, wherein the first P. jirovecii mitochondrial genecomprises the sequence of SEQ ID NO: 29 or an RNA sequence that is ofthe same length as SEQ ID NO: 29 and is at least 95% identical to SEQ IDNO:
 29. 43. The kit of claim 36, wherein when the first P. jiroveciimitochondrial gene comprises the sequence of SEQ ID NO: 14, SEQ ID NO:19 or SEQ ID NO: 24, or an RNA sequence that is of the same length asSEQ ID NO: 14, SEQ ID NO: 19, or SEQ ID NO: 24 and is at least 95%identical to SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 24,respectively.
 44. The kit of claim 37, wherein the second P. jiroveciimitochondrial gene is comprises the sequence of SEQ ID NO: 9, or an RNAsequence that is of the same length as SEQ ID NO: 9 and is at least 95%identical to SEQ ID NO:
 9. 45. The kit of claim 38, wherein the secondP. jirovecii mitochondrial gene is comprises the sequence of SEQ ID NO:9, or an RNA sequence that is of the same length as SEQ ID NO: 9 and isat least 95% identical to SEQ ID NO:
 9. 46. The kit of claim 34, whereinwhen the first P. jirovecii mitochondrial gene is the gene which codesfor the Cytb protein, the quantification of the RNA transcripts of thefirst P. jirovecii mitochondrial gene is performed using a first probethat hybridizes to SEQ ID NO: 30 or to the complementary sequencethereof, without hybridizing to any of SEQ ID NO: 1, the sequencecomplementary to SEQ ID NO: 1, SEQ ID NO: 2 and the sequencecomplementary to SEQ ID NO: 2; and wherein when the first P. jiroveciimitochondrial gene is the mitochondrial P. jirovecii Small Sub-Unit(mtSSU) gene, the quantification of the RNA transcripts of the first P.jirovecii mitochondrial gene is performed using a first probe thathybridizes to SEQ ID NO: 15, or to the sequence complementary to SEQ IDNO: 15, or to SEQ ID NO: 20, or to the sequence complementary to SEQ IDNO: 20, or to SEQ ID NO: 25, or to the sequence complementary to SEQ IDNO: 25, without hybridizing to any of SEQ ID NO: 3, the sequencecomplementary to SEQ ID NO: 3, SEQ ID NO: 1 and the sequencecomplementary to SEQ ID NO: 1; and wherein when the second P. jiroveciimitochondrial gene is the mitochondrial P. jirovecii Large Sub-Unit(mtLSU) gene, the quantification of the RNA transcripts of the second P.jirovecii mitochondrial gene is performed using a second probe thathybridizes to SEQ ID NO: 10 or to the sequence complementary to SEQ IDNO: 10, without hybridizing to any of SEQ ID NO: 3, the sequencecomplementary to SEQ ID NO: 3, SEQ ID NO: 2 and the sequencecomplementary to SEQ ID NO:
 2. 47. The kit of claim 46, wherein thesecond probe comprises SEQ ID NO:
 13. 48. The kit of claim 46,comprising a primer comprising SEQ ID NO: 11 and a primer comprising SEQID NO: 12.